Living-fossil Research Articles

Genomic data and ecological niche modeling reveal an unusually slow rate of molecular evolution in the Cretaceous Eupteleaceae.

Living fossils are evidence of long-term sustained ecological success. However, whether living fossils have little molecular changes remains poorly known, particularly in plants. Here, we have introduced a novel method that integrates phylogenomic, comparative genomic, and ecological niche modeling analyses to investigate the rate of molecular evolution of Eupteleaceae, a Cretaceous relict angiosperm family endemic to East Asia. We assembled a high-quality chromosome-level nuclear genome, and the chloroplast and mitochondrial genomes of a member of Eupteleaceae (Euptelea pleiosperma). Our results show that Eupteleaceae is most basal in Ranunculales, the earliest-diverging order in eudicots, and shares an ancient whole-genome duplication event with the other Ranunculales. We document that Eupteleaceae has the slowest rate of molecular changes in the observed angiosperms. The unusually low rate of molecular evolution of Eupteleaceae across all three independent inherited genomes and genes within each of the three genomes is in association with its conserved genome architecture, ancestral woody habit, and conserved niche requirements. Our findings reveal the evolution and adaptation of living fossil plants through large-scale environmental change and also provide new insights into early eudicot diversification.

Genome sequences and population genomics provide insights into the demographic history, inbreeding, and mutation load of two 'living fossil' tree species of Dipteronia.

'Living fossils', that is, ancient lineages of low taxonomic diversity, represent an exceptional evolutionary heritage, yet we know little about how demographic history and deleterious mutation load have affected their long-term survival and extinction risk. We performed whole-genome sequencing and population genomic analyses on Dipteronia sinensis and D. dyeriana, two East Asian Tertiary relict trees. We found large-scale genome reorganizations and identified species-specific genes under positive selection that are likely involved in adaptation. Our demographic analyses suggest that the wider-ranged D. sinensis repeatedly recovered from population bottlenecks over late Tertiary/Quaternary periods of adverse climate conditions, while the population size of the narrow-ranged D. dyeriana steadily decreased since the late Miocene, especially after the Last Glacial Maximum (LGM). We conclude that the efficient purging of deleterious mutations in D. sinensis facilitated its survival and repeated demographic recovery. By contrast, in D. dyeriana, increased genetic drift and reduced selection efficacy, due to recent severe population bottlenecks and a likely preponderance of vegetative propagation, resulted in fixation of strongly deleterious mutations, reduced fitness, and continuous population decline, with likely detrimental consequences for the species' future viability and adaptive potential. Overall, our findings highlight the significant impact of demographic history on levels of accumulation and purging of putatively deleterious mutations that likely determine the long-term survival and extinction risk of Tertiary relict trees.

The Epistemic Value of the Living Fossils Concept

Living fossils, taxa with similar members now and in the deep past, have recently come under scrutiny. Those who think the concept should be retained have argued for its epistemic and normative utility. This article extends the epistemic utility of the living fossils concept to include ways in which a taxon’s living fossil status can serve as evidence for other claims about that taxon. I will use insights from developmental biology to refine these claims. Insofar as these considerations demonstrate the epistemic utility of the living fossils concept, they support retaining the concept and using it in biological research.

Genomic insights on the contribution of balancing selection and local adaptation to the long-term survival of a widespread living fossil tree, Cercidiphyllum japonicum.

'Living fossils' are testimonies of long-term sustained ecological success, but how demographic history and natural selection contributed to their survival, resilience, and persistence in the face of Quaternary climate fluctuations remains unclear. To better understand the interplay between demographic history and selection in shaping genomic diversity and evolution of such organisms, we assembled the whole genome of Cercidiphyllum japonicum, a widespread East Asian Tertiary relict tree, and resequenced 99 individuals of C.japonicum and its sister species, Cercidiphyllum magnificum (Central Japan). We dated this speciation event to the mid-Miocene, and the intraspecific lineage divergence of C.japonicum (China vs Japan) to the Early Pliocene. Throughout climatic upheavals of the late Tertiary/Quaternary, population bottlenecks greatly reduced the genetic diversity of C.japonicum. However, this polymorphism loss was likely counteracted by, first, long-term balancing selection at multiple chromosomal and heterozygous gene regions, potentially reflecting overdominance, and, second, selective sweeps at stress response and growth-related genes likely involved in local adaptation. Our findings contribute to a better understanding of how living fossils have survived climatic upheaval and maintained an extensive geographic range; that is, both types of selection could be major factors contributing to the species' survival, resilience, and persistence.

Quantifying the living fossil concept

“Living fossil” is a contentious label, often used to identify clades that have experienced particularly little evolutionary change. Many of the problems associated with the term are due to a lack of a clear definition. To date, most work on the phenomenon has been primarily qualitative, leading to a list of living fossils each selected for different sets of reasons. This non-uniformity in living fossil identification makes the ubiquity, clarity and potential causes of the phenomenon difficult to assess. An alternative approach is to use a quantitative metric that matches the most common interpretations of “living fossil” to generate a less subjective listing. Here, we present the Evolutionary Performance Index (EPI); this metric is calculable across the entire tree of life and allows for fair comparisons between taxonomic groups. With this index, we calculated the performance scores for over 24,000 clades within Metazoa and Embryophyta. Many well-known living fossils featured among the lowest performing clades, e.g. coelacanths, gingko, tuataras, as well as groups that have previously been overlooked. By grounding the definition in a strictly quantitative framework, future researchers will be better able to test the causes and relevance of the phenomenon.

Genomic signatures of evolution in Nautilus-An endangered living fossil.

Living fossils are survivors of previously more diverse lineages that originated millions of years ago and persisted with little morphological change. Therefore, living fossils are model organisms to study both long-term and ongoing adaptation and speciation processes. However, many aspects of living fossil evolution and their persistence in the modern world remain unclear. Here, we investigate three major aspects of the evolutionary history of living fossils: cryptic speciation, population genetics and effective population sizes, using members of the genera Nautilus and Allonautilus as classic examples of true living fossils. For this, we analysed genomewide ddRAD-Seq data for all six currently recognized nautiloid species throughout their distribution range. Our analyses identified three major allopatric Nautilus clades: a South Pacific clade, subdivided into three subclades with no signs of admixture between them; a Coral Sea clade, consisting of two genetically distinct populations with significant admixture; and a widespread Indo-Pacific clade, devoid of significant genetic substructure. Within these major clades, we detected five Nautilus groups, which likely correspond to five distinct species. With the exception of Nautilus macromphalus, all previously described species are at odds with genomewide data, testifying to the prevalence of cryptic species among living fossils. Detailed FST analyses further revealed significant genome-wide and locus-specific signatures of selection between species and differentiated populations, which is demonstrated here for the first time in a living fossil. Finally, approximate Bayesian computation (ABC) simulations suggest large effective population sizes, which may explain the low levels of population differentiation commonly observed in living fossils.

Analysis of the cytochrome c oxidase subunit 1 (COX1) gene reveals the unique evolution of the giant panda

As the rate-limiting enzyme of the mitochondrial respiratory chain, cytochrome c oxidase (COX) plays a crucial role in biological metabolism. “Living fossil” giant panda (Ailuropoda melanoleuca) is well-known for its special bamboo diet. In an effort to explore functional variation of COX1 in the energy metabolism behind giant panda's low-energy bamboo diet, we looked at genetic variation of COX1 gene in giant panda, and tested for its selection effect. In 1545 base pairs of the gene from 15 samples, 9 positions were variable and 1 mutation leaded to an amino acid sequence change. COX1 gene produces six haplotypes, nucleotide (pi), haplotype diversity (Hd). In addition, the average number of nucleotide differences (k) is 0.001629±0.001036, 0.8083±0.0694 and 2.517, respectively. Also, dN/dS ratio is significantly below 1. These results indicated that giant panda had a low population genetic diversity, and an obvious purifying selection of the COX1 gene which reduces synthesis of ATP determines giant panda's low-energy bamboo diet. Phylogenetic trees based on the COX1 gene were constructed to demonstrate that giant panda is the sister group of other Ursidae.

Extant primitively segmented spiders have recently diversified from an ancient lineage.

Living fossils are lineages that have retained plesiomorphic traits through long time periods. It is expected that such lineages have both originated and diversified long ago. Such expectations have recently been challenged in some textbook examples of living fossils, notably in extant cycads and coelacanths. Using a phylogenetic approach, we tested the patterns of the origin and diversification of liphistiid spiders, a clade of spiders considered to be living fossils due to their retention of arachnid plesiomorphies and their exclusive grouping in Mesothelae, an ancient clade sister to all modern spiders. Facilitated by original sampling throughout their Asian range, we here provide the phylogenetic framework necessary for reconstructing liphistiid biogeographic history. All phylogenetic analyses support the monophyly of Liphistiidae and of eight genera. As the fossil evidence supports a Carboniferous Euramerican origin of Mesothelae, our dating analyses postulate a long eastward over-land dispersal towards the Asian origin of Liphistiidae during the Palaeogene (39-58 Ma). Contrary to expectations, diversification within extant liphistiid genera is relatively recent, in the Neogene and Late Palaeogene (4-24 Ma). While no over-water dispersal events are needed to explain their evolutionary history, the history of liphistiid spiders has the potential to play prominently in vicariant biogeographic studies.

Living fossils in the Indo-Pacific warm pool: A refuge for thermophilic dinoflagellates during glaciations

Research Article| June 01, 2014 Living fossils in the Indo-Pacific warm pool: A refuge for thermophilic dinoflagellates during glaciations Kenneth N. Mertens; Kenneth N. Mertens 1Research Unit for Palaeontology, Ghent University, Krijgslaan 281 S8, Ghent 9000, Belgium Search for other works by this author on: GSW Google Scholar Yoshihito Takano; Yoshihito Takano 2Institute for East China Sea Research (ECSER), Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan Search for other works by this author on: GSW Google Scholar Martin J. Head; Martin J. Head 3Department of Earth Sciences, Brock University, 500 Glenridge Avenue, St. Catharines, Ontario L2S 3A1, Canada Search for other works by this author on: GSW Google Scholar Kazumi Matsuoka Kazumi Matsuoka 2Institute for East China Sea Research (ECSER), Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan Search for other works by this author on: GSW Google Scholar Author and Article Information Kenneth N. Mertens 1Research Unit for Palaeontology, Ghent University, Krijgslaan 281 S8, Ghent 9000, Belgium Yoshihito Takano 2Institute for East China Sea Research (ECSER), Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan Martin J. Head 3Department of Earth Sciences, Brock University, 500 Glenridge Avenue, St. Catharines, Ontario L2S 3A1, Canada Kazumi Matsuoka 2Institute for East China Sea Research (ECSER), Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan Publisher: Geological Society of America Received: 11 Jan 2014 Revision Received: 25 Mar 2014 Accepted: 26 Mar 2014 First Online: 09 Mar 2017 Online ISSN: 1943-2682 Print ISSN: 0091-7613 © 2014 Geological Society of America Geology (2014) 42 (6): 531–534. https://doi.org/10.1130/G35456.1 Article history Received: 11 Jan 2014 Revision Received: 25 Mar 2014 Accepted: 26 Mar 2014 First Online: 09 Mar 2017 Cite View This Citation Add to Citation Manager Share Icon Share Facebook Twitter LinkedIn MailTo Tools Icon Tools Get Permissions Search Site Citation Kenneth N. Mertens, Yoshihito Takano, Martin J. Head, Kazumi Matsuoka; Living fossils in the Indo-Pacific warm pool: A refuge for thermophilic dinoflagellates during glaciations. Geology 2014;; 42 (6): 531–534. doi: https://doi.org/10.1130/G35456.1 Download citation file: Ris (Zotero) Refmanager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentBy SocietyGeology Search Advanced Search Abstract How important are refugia for plankton biogeography? Here for the first time we report living cysts of the fossil dinoflagellate Dapsilidinium pastielsii from Southeast Asia: Shioya Bay (Okinawa, Japan), Koror (Palau), Ambon (Indonesia), East Vietnam Sea (Vietnam), and Masinloc (the Philippines). This species, thought to have become extinct in the early Pleistocene, is the last survivor of a major early Cenozoic lineage. Its disappearance from the Atlantic following the early Pleistocene implies cooling, and the discovery of living D. pastielsii in the Indo-Pacific warm pool suggests that this unique environment with stable temperatures served as an important refuge for thermophilic dinoflagellates with a >50 m.y. lineage. This is the first record of a refugium plankton species within the Indo-Pacific warm pool. You do not have access to this content, please speak to your institutional administrator if you feel you should have access.

Exploring the Ways of the Plant

Five of the six floristic kingdoms on Earth contribute to the formation of the terrestrial flora and vegetation of the continents surrounding the Pacific Ocean and its islands – ‘Pacifica’. Within the region, extremes of climate and an extraordinarily complex geological history have led to one of the most diverse assemblages of living organisms on the planet. There are good biogeographical reasons why the unique taxonomic history and ecological complexity of the Pacific flora continue to attract the attention of life scientists worldwide: Pacifica includes the world’s longest continuous latitudinal gradient (> 60° N to > 55° S) of vegetation, stretching from the Arctic to the southern tip of the tropical Malaysian peninsula in Asia, to southernmost South America and the sub-antarctic islands. The longitudinal gradient reflects continentality on both sides of the Pacific, with vegetation that includes the Arctic, the humid subtropical and warm-temperate evergreen forests of southeastern China and Japan, the complex tropical forests of eastern Indomalesia, the Australian and Chilean sclerophyll forests, the Andean deserts of South America, the temperate rainforests of northwestern North America, and the cold steppes in western North America. Many of the so-called “Living fossils” that reflect the evolutionary history of the Earth’s biota are found in Pacifica. The flora of Pacifica has not only served as an intergenerational focus for scientific study but continues to inspire original concepts and principles that, through researchers such as Darwin and Takhtajan, create such a resounding impact on science. Over the centuries, researchers have been captured by the unique diversity of Pacifica and the intricate web of evolutionary relationships between humankind and plants. Apart from natural evolutionary processes, human culture is one of the most significant determinants of modern vegetation that, when combined with natural processes in Pacifica, is unique within a global context. Inspired by the flora and vegetation of Pacifica, we consider it our duty to draw the attention of researchers 1 Botanical Garden-Institute FEB RAS, Vladivostok 690024 Russia, krestov@biosoil.ru, v_bak@list.ru 2 Institute of Biology and Soil Science FEB RAS, Vladivostok 690022 Russia, krestov@biosoil.ru, v_bak@list.ru 3 Center for Biodiversity Management, P.O. Box 120, Yungaburra, Queensland, 4884 Australia, E-mail: andyg@cbmglobe.org 4 University of Georgia, Athens, Georgia, USA, boxeo@uga.edu

Appropriated pasts: indigenous peoples and the colonial culture of archaeology

Chapter 1 Colonial Culture of Archaeology Chapter 2 Progressivism: The Invention of Prehistory Chapter 3 Antiquation: Aboriginal Peoples as Living Fossils Chapter 4 Migrationism: The Archaeology of Dispossession Chapter 5 Diffusionism: The Archaeology of Alienation Chapter 6 Subjectation: Appropration Through Science Chapter 7 Shared Nations: The New Appropriation Chapter 8 Partnerships: Pathways to a Decolonised Practice Chapter 9 References Chapter 10 Index

Long survival of “living fossils” with low taxonomic diversities in an evolving food web

Living fossils are taxonomic groups surviving for a long time without any remarkable morphological change. Most of them retain low taxonomic diversities. Although some of them have survived in refuges to avoid predators and competitors, not all living fossils live in refuges. The survival of these groups, therefore, should be discussed in the context of biological interaction. I carried out computer simulations of a model food web system, in which each species feeds on others according to its feeding preference. The system evolves via evolution of species. In the simulation, some clades, like “living fossils,” survived for a long time with low species diversities. Such clades consisted of species with low evolutionary rates, which result in high predation pressure and intraclade competition for food. Nevertheless, the clades sustainably utilize prey clades and are consequently provided with sufficient food. In addition, because of the low species diversities of the clades, predators of the clades soon become extinct through lack of food. This study strongly suggests that in an evolving food web system, the low evolutionary rates of living fossils allow the long survival of those groups with low taxonomic diversities.

Living coelacanths:values, eco-ethics and human responsibility

Coelacanths Latllnena chalumnae are the only liv~ng representatives of crossopterygian fish close to the roots of our own vertebrate history and therefore occupy a unique positlon among living fossils. L. chalun~nae has become a synonym for long evolutionary age, timeless existence, tenacity, immortality and links to old roots, appearing in language, poetry, fiction and many art forms. It is a symbol of a new national identity in the Cornoro Archipelago, Western Indian Ocean. I consider here the Intrinsic and extrinsic value of coelacanths and the role of these fish in blodiversity conservation. The fate of coelacanths lies in our hands. It wlll be a measure of the success or failure of 'eco-ethics' as recently defined and called for by ecologists. KEY WORDSLatimeria . Conservation Living fossil

THE PRINCIPALITY OF LIECHTENSTEIN ‐ A LIVING FOSSIL FROM THE TIME OF THE HOLY ROMAN EMPIRE?

German Life and LettersVolume 42, Issue 1 p. 72-90 THE PRINCIPALITY OF LIECHTENSTEIN - A LIVING FOSSIL FROM THE TIME OF THE HOLY ROMAN EMPIRE? Graham Martin, Graham MartinSearch for more papers by this author Graham Martin, Graham MartinSearch for more papers by this author First published: October 1988 https://doi.org/10.1111/j.1468-0483.1988.tb01288.xRead the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Volume42, Issue1October 1988Pages 72-90 RelatedInformation

Status of an Asiatic Member of the Juglandaceae Regarded as a 'Living Fossil'

American Journal of BotanyVolume 40, Issue 9 p. 666-669 Article STATUS OF AN ASIATIC MEMBER OF THE JUGLANDACEAE REGARDED AS A ‘LIVING FOSSIL' Richard A. Scott, Richard A. Scott Department of Botany, University of Michigan, Ann Arbor, MichiganPresent address: The Biological Laboratories, Harvard University.Search for more papers by this author Richard A. Scott, Richard A. Scott Department of Botany, University of Michigan, Ann Arbor, MichiganPresent address: The Biological Laboratories, Harvard University.Search for more papers by this author First published: 01 November 1953 https://doi.org/10.1002/j.1537-2197.1953.tb06538.xCitations: 3 AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Citing Literature Volume40, Issue9November 1953Pages 666-669 RelatedInformation