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Vaill M, Kawanishi K, Varki N, Gagneux P, Varki A. Comparative physiological anthropogeny: exploring molecular underpinnings of distinctly human phenotypes. Physiol Rev 2023; 103:2171-2229. [PMID: 36603157 PMCID: PMC10151058 DOI: 10.1152/physrev.00040.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Anthropogeny is a classic term encompassing transdisciplinary investigations of the origins of the human species. Comparative anthropogeny is a systematic comparison of humans and other living nonhuman hominids (so-called "great apes"), aiming to identify distinctly human features in health and disease, with the overall goal of explaining human origins. We begin with a historical perspective, briefly describing how the field progressed from the earliest evolutionary insights to the current emphasis on in-depth molecular and genomic investigations of "human-specific" biology and an increased appreciation for cultural impacts on human biology. While many such genetic differences between humans and other hominids have been revealed over the last two decades, this information remains insufficient to explain the most distinctive phenotypic traits distinguishing humans from other living hominids. Here we undertake a complementary approach of "comparative physiological anthropogeny," along the lines of the preclinical medical curriculum, i.e., beginning with anatomy and considering each physiological system and in each case considering genetic and molecular components that are relevant. What is ultimately needed is a systematic comparative approach at all levels from molecular to physiological to sociocultural, building networks of related information, drawing inferences, and generating testable hypotheses. The concluding section will touch on distinctive considerations in the study of human evolution, including the importance of gene-culture interactions.
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Affiliation(s)
- Michael Vaill
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
| | - Kunio Kawanishi
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Department of Experimental Pathology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Nissi Varki
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Pascal Gagneux
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Ajit Varki
- Center for Academic Research and Training in Anthropogeny, University of California, San Diego, La Jolla, California
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California
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2
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Pozzi L, Penna A. Rocks and clocks revised: New promises and challenges in dating the primate tree of life. Evol Anthropol 2022; 31:138-153. [PMID: 35102633 DOI: 10.1002/evan.21940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 10/04/2021] [Accepted: 01/12/2022] [Indexed: 01/14/2023]
Abstract
In recent years, multiple technological and methodological advances have increased our ability to estimate phylogenies, leading to more accurate dating of the primate tree of life. Here we provide an overview of the limitations and potentials of some of these advancements and discuss how dated phylogenies provide the crucial temporal scale required to understand primate evolution. First, we review new methods, such as the total-evidence dating approach, that promise a better integration between the fossil record and molecular data. We then explore how the ever-increasing availability of genomic-level data for more primate species can impact our ability to accurately estimate timetrees. Finally, we discuss more recent applications of mutation rates to date divergence times. We highlight example studies that have applied these approaches to estimate divergence dates within primates. Our goal is to provide a critical overview of these new developments and explore the promises and challenges of their application in evolutionary anthropology.
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Affiliation(s)
- Luca Pozzi
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Anna Penna
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
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3
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Marciniak S, Mughal MR, Godfrey LR, Bankoff RJ, Randrianatoandro H, Crowley BE, Bergey CM, Muldoon KM, Randrianasy J, Raharivololona BM, Schuster SC, Malhi RS, Yoder AD, Louis EE, Kistler L, Perry GH. Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant, "subfossil" koala lemur Megaladapis edwardsi. Proc Natl Acad Sci U S A 2021; 118:e2022117118. [PMID: 34162703 PMCID: PMC8255780 DOI: 10.1073/pnas.2022117118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
No endemic Madagascar animal with body mass >10 kg survived a relatively recent wave of extinction on the island. From morphological and isotopic analyses of skeletal "subfossil" remains we can reconstruct some of the biology and behavioral ecology of giant lemurs (primates; up to ∼160 kg) and other extraordinary Malagasy megafauna that survived into the past millennium. Yet, much about the evolutionary biology of these now-extinct species remains unknown, along with persistent phylogenetic uncertainty in some cases. Thankfully, despite the challenges of DNA preservation in tropical and subtropical environments, technical advances have enabled the recovery of ancient DNA from some Malagasy subfossil specimens. Here, we present a nuclear genome sequence (∼2× coverage) for one of the largest extinct lemurs, the koala lemur Megaladapis edwardsi (∼85 kg). To support the testing of key phylogenetic and evolutionary hypotheses, we also generated high-coverage nuclear genomes for two extant lemurs, Eulemur rufifrons and Lepilemur mustelinus, and we aligned these sequences with previously published genomes for three other extant lemurs and 47 nonlemur vertebrates. Our phylogenetic results confirm that Megaladapis is most closely related to the extant Lemuridae (typified in our analysis by E. rufifrons) to the exclusion of L. mustelinus, which contradicts morphology-based phylogenies. Our evolutionary analyses identified significant convergent evolution between M. edwardsi and an extant folivore (a colobine monkey) and an herbivore (horse) in genes encoding proteins that function in plant toxin biodegradation and nutrient absorption. These results suggest that koala lemurs were highly adapted to a leaf-based diet, which may also explain their convergent craniodental morphology with the small-bodied folivore Lepilemur.
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Affiliation(s)
- Stephanie Marciniak
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
| | - Mehreen R Mughal
- Bioinformatics and Genomics Intercollege Graduate Program, Pennsylvania State University, University Park, PA 16082
| | - Laurie R Godfrey
- Department of Anthropology, University of Massachusetts, Amherst, MA 01003
| | - Richard J Bankoff
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
| | - Heritiana Randrianatoandro
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Mention Anthropobiologie et Développement Durable, Faculté des Sciences, Université d'Antananarivo, Antananarivo 101, Madagascar
| | - Brooke E Crowley
- Department of Geology, University of Cincinnati, Cincinnati, OH 45220
- Department of Anthropology, University of Cincinnati, Cincinnati, OH 45220
| | - Christina M Bergey
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Department of Genetics, Rutgers University, New Brunswick, NJ 08854
| | | | - Jeannot Randrianasy
- Mention Anthropobiologie et Développement Durable, Faculté des Sciences, Université d'Antananarivo, Antananarivo 101, Madagascar
| | - Brigitte M Raharivololona
- Mention Anthropobiologie et Développement Durable, Faculté des Sciences, Université d'Antananarivo, Antananarivo 101, Madagascar
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 639798
| | - Ripan S Malhi
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL 61801
- Department of Ecology, Evolution and Behavior, Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC 27708
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708
| | - Edward E Louis
- Department of Conservation Genetics, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107;
| | - Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560;
| | - George H Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802;
- Bioinformatics and Genomics Intercollege Graduate Program, Pennsylvania State University, University Park, PA 16082
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
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Weiss CV, Harshman L, Inoue F, Fraser HB, Petrov DA, Ahituv N, Gokhman D. The cis-regulatory effects of modern human-specific variants. eLife 2021; 10:e63713. [PMID: 33885362 PMCID: PMC8062137 DOI: 10.7554/elife.63713] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 03/30/2021] [Indexed: 12/24/2022] Open
Abstract
The Neanderthal and Denisovan genomes enabled the discovery of sequences that differ between modern and archaic humans, the majority of which are noncoding. However, our understanding of the regulatory consequences of these differences remains limited, in part due to the decay of regulatory marks in ancient samples. Here, we used a massively parallel reporter assay in embryonic stem cells, neural progenitor cells, and bone osteoblasts to investigate the regulatory effects of the 14,042 single-nucleotide modern human-specific variants. Overall, 1791 (13%) of sequences containing these variants showed active regulatory activity, and 407 (23%) of these drove differential expression between human groups. Differentially active sequences were associated with divergent transcription factor binding motifs, and with genes enriched for vocal tract and brain anatomy and function. This work provides insight into the regulatory function of variants that emerged along the modern human lineage and the recent evolution of human gene expression.
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Affiliation(s)
- Carly V Weiss
- Department of Biology, Stanford University, StanfordStanfordUnited States
| | - Lana Harshman
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San FranciscoSan FranciscoUnited States
- Institute for Human Genetics, University of California San Francisco, San FranciscoSan FranciscoUnited States
| | - Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San FranciscoSan FranciscoUnited States
- Institute for Human Genetics, University of California San Francisco, San FranciscoSan FranciscoUnited States
| | - Hunter B Fraser
- Department of Biology, Stanford University, StanfordStanfordUnited States
| | - Dmitri A Petrov
- Department of Biology, Stanford University, StanfordStanfordUnited States
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San FranciscoSan FranciscoUnited States
- Institute for Human Genetics, University of California San Francisco, San FranciscoSan FranciscoUnited States
| | - David Gokhman
- Department of Biology, Stanford University, StanfordStanfordUnited States
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Hernandez M, Perry GH. Scanning the human genome for "signatures" of positive selection: Transformative opportunities and ethical obligations. Evol Anthropol 2021; 30:113-121. [PMID: 33788352 DOI: 10.1002/evan.21893] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 01/25/2021] [Accepted: 03/11/2021] [Indexed: 12/15/2022]
Abstract
The relationship history of evolutionary anthropology and genetics is complex. At best, genetics is a beautifully integrative part of the discipline. Yet this integration has also been fraught, with punctuated, disruptive challenges to dogma, periodic reluctance by some members of the field to embrace results from analyses of genetic data, and occasional over-assertions of genetic definitiveness by geneticists. At worst, evolutionary genetics has been a tool for reinforcing racism and colonialism. While a number of genetics/genomics papers have disproportionately impacted evolutionary anthropology, here we highlight the 2002 presentation of an elegantly powerful approach for identifying "signatures" of past positive selection from haplotype-based patterns of genetic variation. Together with technological advances in genotyping methods, this article transformed our field by facilitating genome-wide "scans" for signatures of past positive selection in human populations. This approach helped researchers test longstanding evolutionary anthropology hypotheses while simultaneously providing opportunities to develop entirely new ones. Genome-wide scans for signatures of positive selection have since been conducted in diverse worldwide populations, with striking findings of local adaptation and convergent evolution. Yet there are ethical considerations with respect to the ubiquity of these studies and the cross-application of the genome-wide scan approach to existing datasets, which we also discuss.
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Affiliation(s)
- Margarita Hernandez
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - George H Perry
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
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Meng J, Liu J, Chen D, Kang J, Huang Y, Li D, Duan Y, Wang J. Integration of lncRNA and mRNA profiles to reveal the protective effects of Codonopsis pilosula extract on the gastrointestinal tract of mice subjected to D‑galactose‑induced aging. Int J Mol Med 2021; 47:1. [PMID: 33448313 PMCID: PMC7834956 DOI: 10.3892/ijmm.2020.4834] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
Codonopsis pilosula is a type of traditional Chinese medicine that exerts an anti‑aging effect and can regulate the gastrointestinal (GI) system. The aim of the present study was to investigate the underlying molecular mechanisms responsible for the anti‑aging effects of Codonopsis pilosula in the GI tract of mice with D‑galactose‑induced aging. First, a successful mouse model of aging was established, and Codonopsis pilosula water extract was then used for treatment. The anti‑aging effects of Codonopsis pilosula on the GI tract were then detected from the perspectives of tissue structure, physiological function and cell ultrastructure. Finally, in order to explore the underlying molecular mechanisms, the expression profiles of lncRNAs and mRNAs in the stomach and intestine were examined using microarray technology. A total of 117 (41 lncRNAs and 76 mRNAs) and 168 (85 lncRNA sand 83 mRNAs) differentially expressed genes associated with the anti‑aging effects of Codonopsis pilosula were identified in the stomach and intestine, respectively. Through integrated analysis of the stomach and intestine, 4 hub RNAs, including 1 lncRNA (LOC105243318) and 3 mRNAs (Fam132a, Rorc and 1200016E24Rik) were identified, which may be associated with the anti‑aging effects of Codonopsis pilosula in the GI tract of aging mice. The Kyoto Encyclopedia of Genes and Genomes analysis revealed that the metabolic pathway was an important pathway underlying the anti‑aging effects of Codonopsis pilosula in the GI tract. On the whole, in the present study, 4 hub RNAs associated with these effects and their regulatory networks were found in the GI tract of aging mice. In addition, the metabolic pathway was found to play an important role in these anti‑aging effects in the GI tract.
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Affiliation(s)
- Jie Meng
- College of Clinical Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu 730000, P.R. China
| | - Jiajia Liu
- College of Clinical Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu 730000, P.R. China
| | - Dongmei Chen
- College of Clinical Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu 730000, P.R. China
| | - Jiachao Kang
- College of Clinical Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu 730000, P.R. China
| | - Yong Huang
- College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu 730000, P.R. China
| | - Dandan Li
- College of Clinical Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu 730000, P.R. China
| | - Yongqiang Duan
- College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu 730000, P.R. China
| | - Jing Wang
- College of Clinical Medicine, Gansu University of Chinese Medicine, Lanzhou, Gansu 730000, P.R. China
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Abstract
The misuse of sport-related gene transfer methods in elite athletes is a real and growing concern. The success of gene therapy in the treatment of hereditary diseases has been most evident since targets in gene therapy products can be used in healthy individuals to improve sports performance. Performing these practices threatens the sporting character of competitions and may pose potential health hazards. Since the World Anti-Doping Agency pronouncement on the prohibition of such practices in 2003, several researchers have been trying to address the challenge of developing an effective method for the detection of genetic doping. This review presents an overview of the published methods developed for this purpose, the advantages and limitations of technologies and the putative target genes. At last, we present the perspective related to the application of the detection methods in the doping control field.
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