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Jernvall J, Di-Poï N, Mikkola ML, Kratochwil CF. Toward a universal measure of robustness across model organs and systems. Evol Dev 2023; 25:410-417. [PMID: 37070415 DOI: 10.1111/ede.12436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 04/03/2023] [Accepted: 04/09/2023] [Indexed: 04/19/2023]
Abstract
The development of an individual must be capable of resisting the harmful effects of internal and external perturbations. This capacity, called robustness, can make the difference between normal variation and disease. Some systems and organs are more resilient in their capacity to correct the effects of internal disturbances such as mutations. Similarly, organs and organisms differ in their capacity to be resilient against external disturbances, such as changes in temperature. Furthermore, all developmental systems must be somewhat flexible to permit evolutionary change, and understanding robustness requires a comparative framework. Over the last decades, most research on developmental robustness has been focusing on specific model systems and organs. Hence, we lack tools that would allow cross-species and cross-organ comparisons. Here, we emphasize the need for a uniform framework to experimentally test and quantify robustness across study systems and suggest that the analysis of fluctuating asymmetry might be a powerful proxy to do so. Such a comparative framework will ultimately help to resolve why and how organs of the same and different species differ in their sensitivity to internal (e.g., mutations) and external (e.g., temperature) perturbations and at what level of biological organization buffering capacities exist and therefore create robustness of the developmental system.
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Affiliation(s)
- Jukka Jernvall
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Nicolas Di-Poï
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Marja L Mikkola
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
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2
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Sundell T, Kammonen JI, Mustanoja E, Biard V, Kunnasranta M, Niemi M, Nykänen M, Nyman T, Palo JU, Valtonen M, Paulin L, Jernvall J, Auvinen P. Genomic evidence uncovers inbreeding and supports translocations in rescuing the genetic diversity of a landlocked seal population. CONSERV GENET 2023. [DOI: 10.1007/s10592-022-01497-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
AbstractFragmentation of isolated populations increases the risk of inbreeding and loss of genetic diversity. The endemic Saimaa ringed seal (Pusa hispida saimensis) is one of the most endangered pinnipeds in the world with a population of only ~ 400 individuals. The current genetic diversity of this subspecies, isolated in Lake Saimaa in Finland for ca. 1000 generations, is alarmingly low. We performed whole-genome sequencing on Saimaa ringed seals (N = 30) and analyzed the level of homozygosity and genetic composition across the individual genomes. Our results show that the Saimaa ringed seal population has a high number of runs of homozygosity (RoH) compared with the neighboring Baltic ringed seal (Pusa hispida botnica) reference population (p < 0.001). There is also a tendency for stillborn seal pups to have more pronounced RoH. Since the population is divided into semi-isolated subpopulations within the Lake Saimaa exposing the population to deleterious genomic effects, our results support augmented gene flow as a genetic conservation action. Based on our results suggesting inbreeding depression in the population, we recommend Pihlajavesi as a potential source and Southern Saimaa as a potential recipient subpopulation for translocating individuals. The Saimaa ringed seal is a recognized subspecies and therefore translocations should be considered only within the lake to avoid an unpredictable risk of disease, the introduction of deleterious alleles, and severe ecological issues for the population.
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Skull ecomorphological variation of narwhals (Monodon monoceros, Linnaeus 1758) and belugas (Delphinapterus leucas, Pallas 1776) reveals phenotype of their hybrids. PLoS One 2022; 17:e0273122. [PMID: 35960760 PMCID: PMC9374245 DOI: 10.1371/journal.pone.0273122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/03/2022] [Indexed: 11/19/2022] Open
Abstract
Narwhals and belugas are toothed whales belonging to the Monodontidae. Belugas have a circumpolar Arctic and sub-Artic distribution while narwhals are restricted to the Atlantic Arctic. Their geographical ranges overlap during winter migrations in the Baffin Bay area (Canada/West Greenland) and successful interbreeding may occur. Here, we employed geometric morphometrics on museum specimens to explore the cranium and mandible morphology of a known hybrid (NHMD MCE 1356) and the cranium morphology of a putative hybrid (NHMD 1963.44.1.4) relative to skull morphological variation in the parental species. Specifically, we used 3D models of skulls from 69 belugas, 86 narwhals, and the two known/putative hybrids and 2D left hemi-mandibles from 20 belugas, 64 narwhals and the known hybrid. Skull shape analyses allowed clear discrimination between species. Narwhals are characterised by a relatively short rostrum and wide neurocranium while belugas show a more elongated and narrower cranium. Sexual size dimorphism was detected in narwhals, with males larger than females, but no sexual shape dimorphism was detected in either species (excluding presence/absence of tusks in narwhals). Morphological skull variation was also dependent on different allometric slopes between species and sexes in narwhals. Our analyses showed that the cranium of the known hybrid was phenotypically close to belugas but its 2D hemi-mandible had a narwhal shape and size morphology. Both cranium and mandible were strongly correlated, with the pattern of covariation being similar to belugas. The putative hybrid was a pure male narwhal with extruded teeth. Comparison of genomic DNA supported this result, and stable carbon and nitrogen isotope values suggested that the putative hybrid had a more benthic foraging strategy compared to narwhals. This work demonstrates that although the known hybrid could be discriminated from narwhals and belugas, detection of its affinities with these parental species was dependent on the part of the skull analysed.
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Galatius A, Svendsen MS, Messer D, Valtonen M, McGowen M, Sabin R, Dahl VA, Dahl AB, Olsen MT. Range-wide variation in grey seal (Halichoerus grypus) skull morphology. ZOOLOGY 2022; 153:126023. [PMID: 35717730 DOI: 10.1016/j.zool.2022.126023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/26/2022] [Accepted: 06/03/2022] [Indexed: 11/30/2022]
Abstract
The large interspecific variation in marine mammal skull and dental morphology reflects ecological specialisations to foraging and communication. At the intraspecific level, the drivers of skull shape variation are less well understood, having implications for identifying putative local foraging adaptations and delineating populations and subspecies for taxonomy, systematics, management and conservation. Here, we assess the range-wide intraspecific variation in 71 grey seal skulls by 3D surface scanning, collection of cranial landmarks and geometric morphometric analysis. We find that skull shape differs slightly between populations in the Northwest Atlantic, Northeast Atlantic and Baltic Sea. However, there was a large shape overlap between populations and variation was substantially larger among animals within populations than between. We hypothesize that this pattern of intraspecific variation in grey seal skull shape results from balancing selection or phenotypic plasticity allowing for a remarkably generalist foraging behaviour. Moreover, the large overlap in skull shape between populations implies that the separate subspecies status of Atlantic and Baltic Sea grey seals is questionable from a morphological point of view.
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Affiliation(s)
- Anders Galatius
- Marine Mammal Research, Department of Ecoscience, Aarhus University, Denmark.
| | | | - Dolores Messer
- Section for Visual Computing, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Denmark
| | - Mia Valtonen
- Institute of Biotechnology, University of Helsinki, Finland; Wildlife Ecology Group, Natural Resources Institute, Finland
| | - Michael McGowen
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC, USA
| | - Richard Sabin
- Division of Vertebrates, Department of Life Sciences, Natural History Museum, London, UK
| | - Vedrana Andersen Dahl
- Section for Visual Computing, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Denmark
| | - Anders Bjorholm Dahl
- Section for Visual Computing, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Denmark
| | - Morten Tange Olsen
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Denmark; Natural History Museum of Denmark, University of Copenhagen, Denmark.
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5
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Thiery AP, Standing AS, Cooper RL, Fraser GJ. An epithelial signalling centre in sharks supports homology of tooth morphogenesis in vertebrates. eLife 2022; 11:73173. [PMID: 35536602 PMCID: PMC9249395 DOI: 10.7554/elife.73173] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
Development of tooth shape is regulated by the enamel knot signalling centre, at least in mammals. Fgf signalling regulates differential proliferation between the enamel knot and adjacent dental epithelia during tooth development, leading to formation of the dental cusp. The presence of an enamel knot in non-mammalian vertebrates is debated given differences in signalling. Here, we show the conservation and restriction of fgf3, fgf10, and shh to the sites of future dental cusps in the shark (Scyliorhinus canicula), whilst also highlighting striking differences between the shark and mouse. We reveal shifts in tooth size, shape, and cusp number following small molecule perturbations of canonical Wnt signalling. Resulting tooth phenotypes mirror observed effects in mammals, where canonical Wnt has been implicated as an upstream regulator of enamel knot signalling. In silico modelling of shark dental morphogenesis demonstrates how subtle changes in activatory and inhibitory signals can alter tooth shape, resembling developmental phenotypes and cusp shapes observed following experimental Wnt perturbation. Our results support the functional conservation of an enamel knot-like signalling centre throughout vertebrates and suggest that varied tooth types from sharks to mammals follow a similar developmental bauplan. Lineage-specific differences in signalling are not sufficient in refuting homology of this signalling centre, which is likely older than teeth themselves.
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Affiliation(s)
- Alexandre P Thiery
- Department of Animal and Plant Sciences, King's College London, London, United Kingdom
| | - Ariane S Standing
- Department of Biology, University of Florida, Gainesville, United States
| | - Rory L Cooper
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Gareth J Fraser
- Department of Biology, University of Florida, Gainesville, United States
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Genomic evaluation of hybridization in historic and modern North American Bison (Bison bison). Sci Rep 2022; 12:6397. [PMID: 35430616 PMCID: PMC9013353 DOI: 10.1038/s41598-022-09828-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 03/24/2022] [Indexed: 11/17/2022] Open
Abstract
During the late nineteenth century North American bison underwent a significant population bottleneck resulting in a reduction in population size of over 99% and a species-level near-extinction event. Factors responsible for this destruction included indiscriminate killing, loss of access to suitable habitat, and diseases. At the nadir of this population crash, very few wild plains bison survived and were restricted to Yellowstone National Park, USA and a small number of wild wood bison remained in Wood Buffalo National Park, Canada. However, most surviving bison in the late 1800’s were maintained by cattle ranchers in private herds where hybridization between bison with various breeds of domestic cattle was often encouraged. Over the last 20 years, the legacy of this introgression has been identified using mitochondrial DNA and limited nuclear microsatellite analyses. However, no genome-wide assessment has been performed, and some herds were believed to be free of introgression based on current genetic testing strategies. Herein, we report detailed analyses using whole genome sequencing from nineteen modern and six historical bison, chosen to represent the major lineages of bison, to identify and quantitate signatures of nuclear introgression in their recent (within 200 years) history. Both low and high coverage genomes provided evidence for recent introgression, including animals from Yellowstone, Wind Cave, and Elk Island National Parks which were previously thought to be free from hybridization with domestic cattle. We employed multiple approaches, including one developed for this work, to identify putative cattle haplotypes in each bison genome. These regions vary greatly in size and frequency by sample and herd, though we detected domestic cattle introgression in all bison genomes tested. Since our sampling strategy spanned across the diversity of modern bison populations, these finding are best explained by multiple historical hybridization events between these two species with significant genetic recombination over the last 200 years. Our results demonstrate that whole genome sequencing approaches are required to accurately quantitate cattle introgression in bison.
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7
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Liu X, Schjøtt SR, Granquist SM, Rosing-Asvid A, Dietz R, Teilmann J, Galatius A, Cammen K, O Corry-Crowe G, Harding K, Härkönen T, Hall A, Carroll EL, Kobayashi Y, Hammill M, Stenson G, Frie AK, Lydersen C, Kovacs KM, Andersen LW, Hoffman JI, Goodman SJ, Vieira FG, Heller R, Moltke I, Tange Olsen M. Origin and expansion of the world's most widespread pinniped: range-wide population genomics of the harbour seal (Phoca vitulina). Mol Ecol 2022; 31:1682-1699. [PMID: 35068013 PMCID: PMC9306526 DOI: 10.1111/mec.16365] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 11/26/2022]
Abstract
The harbour seal (Phoca vitulina) is the most widely distributed pinniped, occupying a wide variety of habitats and climatic zones across the Northern Hemisphere. Intriguingly, the harbour seal is also one of the most philopatric seals, raising questions as to how it colonised virtually the whole of the Northern Hemisphere. To shed light on the origin, remarkable range expansion, population structure and genetic diversity of this species, we used genotyping-by-sequencing to analyse ~13,500 biallelic SNPs from 286 individuals sampled from 22 localities across the species' range. Our results point to a Northeast Pacific origin, colonisation of the North Atlantic via the Canadian Arctic, and subsequent stepping-stone range expansions across the North Atlantic from North America to Europe, accompanied by a successive loss of genetic diversity. Our analyses further revealed a deep divergence between modern North Pacific and North Atlantic harbour seals, with finer-scale genetic structure at regional and local scales consistent with strong philopatry. The study provides new insights into the harbour seal's remarkable ability to colonise and adapt to a wide range of habitats. Furthermore, it has implications for current harbour seal subspecies delineations and highlights the need for international and national red lists and management plans to ensure the protection of genetically and demographically isolated populations.
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Affiliation(s)
- Xiaodong Liu
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark
| | | | - Sandra M Granquist
- Icelandic Seal Centre, Höfðabraut 6, 530, Hvammstangi, Iceland.,Marine and Freshwater Research Institute, Institute of Freshwater Fisheries Fornubúðir 5, 220, Hafnarfjörður, Iceland
| | | | - Rune Dietz
- Marine Mammal Research, Department of Ecoscience, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Jonas Teilmann
- Marine Mammal Research, Department of Ecoscience, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Anders Galatius
- Marine Mammal Research, Department of Ecoscience, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | | | - Greg O Corry-Crowe
- Wildlife Evolution and Behavior Program, Florida Atlantic University, USA
| | - Karin Harding
- Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
| | | | - Ailsa Hall
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St. Andrews, UK, KY16 8LB
| | - Emma L Carroll
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Yumi Kobayashi
- Laboratory of Animal Ecology, Research Faculty of Agriculture, Hokkaido University, Japan
| | - Mike Hammill
- Maurice Lamontagne Institute, Fisheries and Oceans Canada, P.O. Box 1000, Mont-Joli, QC, Canada
| | - Garry Stenson
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, P.O. Box 5667, St. John's NL, Canada
| | | | | | - Kit M Kovacs
- Norwegian Polar Institute, Fram Centre, 9296, Tromsø, Norway
| | | | - Joseph I Hoffman
- Department of Animal Behaviour, University of Bielefeld, 33501, Bielefeld, Germany.,British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Simon J Goodman
- School of Biology, Faculty of Biological Sciences, University of Leeds, UK
| | - Filipe G Vieira
- Center for Genomic Medicine, Copenhagen University Hospitalet, Denmark
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark
| | - Ida Moltke
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Denmark
| | - Morten Tange Olsen
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Denmark
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8
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Kitchener AC, Hoffmann M, Yamaguchi N, Breitenmoser-Würsten C, Wilting A. A system for designating taxonomic certainty in mammals and other taxa. Mamm Biol 2022. [DOI: 10.1007/s42991-021-00205-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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Savriama Y, Romestaing C, Clair A, Averty L, Ulmann J, Ledevin R, Renaud S. Wild versus lab house mice: Effects of age, diet, and genetics on molar geometry and topography. J Anat 2022; 240:66-83. [PMID: 34333769 PMCID: PMC8655182 DOI: 10.1111/joa.13529] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/20/2021] [Accepted: 07/20/2021] [Indexed: 11/30/2022] Open
Abstract
Molar morphology is shaped by phylogenetic history and adaptive processes related to food processing. Topographic parameters of the occlusal surface, such as sharpness and relief, can be especially informative regarding diet preferences of a species. The occlusal surface can however be deeply modified by wear throughout an animal's life, potentially obliterating other signals. Age being difficult to assess in wild populations, especially small rodents, experimental studies of wear through age in laboratory populations may constitute a powerful way to assess its impact on molar geometry and topography, and to validate descriptors of molar morphology that could mitigate this issue. Molar morphology was therefore quantified using 3D geometric morphometrics and topographic estimates in four groups of house mice: wild-trapped mice, lab-bred offspring of these wild mice, typical laboratory mice, and their hybrids. Three descriptors of the molar morphology were considered: the surface of the whole molar row, the surface of the first upper molar, and a truncated template of the first upper molar mimicking advanced wear. Increasing wear with age was demonstrated in the different groups, with a more pronounced effect in the wild-trapped population. The geometry of the molar row is not only modified by wear, but also by the relative position of the late developing molars on the jaw due to loading during mastication. As a consequence, the alignment of the molars is modified in wild mice, showing a qualitative difference between wild animals and their lab-bred offspring. Results obtained from the lab should thus be transferred with caution to the interpretation of differences in wild populations. Topographic estimates computed for the first upper molar seems to provide more stable parameters than those based on the whole molar row, because issues related to non-planar occlusal surface along the molar row are discarded. The truncated template was proven efficient in discarding the wear effect to focus on genetic differences, allowing an efficient characterization of the hybridization signature between wild and lab mice. Dominance of the wild phenotype for the first molar shape supports that the lab strain evolved in a context of relaxation of the selective pressures related to nutrition.
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Affiliation(s)
| | - Caroline Romestaing
- Laboratoire d'Écologie des Hydrosystèmes Naturels et Anthropisés (LEHNA)ENTPEUniversité de LyonUniversité Claude Bernard Lyon 1UMR 5023 CNRSVilleurbanneFrance
| | - Angéline Clair
- Plateforme Animalerie Conventionnelle et Sauvage Expérimentale de la Doua (ACSED)Fédération de Recherche 3728Université de LyonUniversité Claude Bernard Lyon 1CNRSENS‐LyonINRAEINSAVetAgroSupVilleurbanneFrance
| | - Laetita Averty
- Plateforme Animalerie Conventionnelle et Sauvage Expérimentale de la Doua (ACSED)Fédération de Recherche 3728Université de LyonUniversité Claude Bernard Lyon 1CNRSENS‐LyonINRAEINSAVetAgroSupVilleurbanneFrance
| | - Julie Ulmann
- Plateforme Animalerie Conventionnelle et Sauvage Expérimentale de la Doua (ACSED)Fédération de Recherche 3728Université de LyonUniversité Claude Bernard Lyon 1CNRSENS‐LyonINRAEINSAVetAgroSupVilleurbanneFrance
| | - Ronan Ledevin
- PACEAUMR 5199 CNRSUniversité de BordeauxPessacFrance
| | - Sabrina Renaud
- Laboratoire de Biométrie et Biologie EvolutiveUMR 5558CNRSUniversité Claude Bernard Lyon 1Université de LyonVilleurbanneFrance
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Buck LT, Katz DC, Ackermann RR, Hlusko LJ, Kanthaswamy S, Weaver TD. Effects of hybridization on pelvic morphology: A macaque model. J Hum Evol 2021; 159:103049. [PMID: 34455262 DOI: 10.1016/j.jhevol.2021.103049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/28/2022]
Abstract
Ancient DNA analyses have shown that interbreeding between hominin taxa occurred multiple times. Although admixture is often reflected in skeletal phenotype, the relationship between the two remains poorly understood, hampering interpretation of the hominin fossil record. Direct study of this relationship is often impossible due to the paucity of hominin fossils and difficulties retrieving ancient genetic material. Here, we use a sample of known ancestry hybrids between two closely related nonhuman primate taxa (Indian and Chinese Macaca mulatta) to investigate the effect of admixture on skeletal morphology. We focus on pelvic shape, which has potential fitness implications in hybrids, as mismatches between maternal pelvic and fetal cranial morphology are often fatal to mother and offspring. As the pelvis is also one of the skeletal regions that differs most between Homo sapiens and Neanderthals, investigating the pelvic consequences of interbreeding could be informative regarding the viability of their hybrids. We find that the effect of admixture in M. mulatta is small and proportional to the relatively small morphological difference between the parent taxa. Sexual dimorphism appears to be the main determinant of pelvic shape in M. mulatta. The lack of difference in pelvic shape between Chinese and Indian M. mulatta is in contrast to that between Neanderthals and H. sapiens, despite a similar split time (in generations) between the hybridizing pairs. Greater phenotypic divergence between hominins may relate to adaptations to disparate environments but may also highlight how the unique degree of cultural buffering in hominins allowed for greater neutral divergence. In contrast to some previous work identifying extreme morphologies in first- and second-generation hybrids, here the relationship between pelvic shape and admixture is linear. This linearity may be because most sampled animals have a multigenerational admixture history or because of relatively high constraints on the pelvis compared with other skeletal regions.
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Affiliation(s)
- Laura T Buck
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK; Department of Anthropology, University of California Davis, USA.
| | - David C Katz
- Department of Anthropology, University of California Davis, USA; University of Calgary, Cumming School of Medicine, Canada
| | - Rebecca Rogers Ackermann
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa
| | - Leslea J Hlusko
- Department of Integrative Biology, University of California Berkeley, USA; Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Burgos, Spain
| | - Sree Kanthaswamy
- School of Natural and Mathematical Sciences, Arizona State University, USA
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11
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Pelletier M, Niinimäki S, Salmi AK. Influence of captivity and selection on limb long bone cross-sectional morphology of reindeer. J Morphol 2021; 282:1533-1556. [PMID: 34323317 DOI: 10.1002/jmor.21403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/09/2021] [Accepted: 07/22/2021] [Indexed: 11/10/2022]
Abstract
The emergence of pastoralism and animal husbandry has been a critical point in the history of human evolution. Beyond profound behavioural changes in domesticated animals compared to wild ones, characterising the morphological changes associated with domestication process remains challenging. Because reindeer (Rangifer tarandus) can be considered to still be in the early phases of the domestication process, the study of modern populations provides a unique opportunity to examine the impact of captivity and selective breeding on skeletal changes. In this work, we investigated the morphological changes in long limb bone cross-sections using 137 wild and domestic reindeer individuals bred in free-range, in captivity or used for racing and pulling. The shape and shaft cortical thickness of the six long limb bones (i.e., humerus, radioulna, metacarpal, femur, tibia and metatarsal) were measured using a 2D-geometric morphometrics approach taking into account subspecies, sex, body mass and lifestyle differences. These bones are important to understanding functional morphological changes because they can provide information on feeding and locomotor behaviours, as well as on body propulsion and weight bearing. Apart from the effects of taxonomy, etho-ecology and sex, we have found that captivity and selection induced important variations in the size and body mass of modern reindeer. Our results also showed that patterns of variation in cortical bone thickness of long limb bone cross-sections were strongly impacted by body mass and human-imposed restrictions in roaming. This demonstrates that bone cross-sections can provide information on changes in locomotor, reproductive and feeding behaviours induced by the domestication process. These results are valuable not only for (paleo) biologists studying the impact of captivity and selection in ungulates but also for archaeologists exploring the origins of domestication and early herding strategies.
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Affiliation(s)
- Maxime Pelletier
- Archaeology, History, Culture and Communication Studies, Faculty of Humanities, University of Oulu, Oulu, Finland
| | - Sirpa Niinimäki
- Archaeology, History, Culture and Communication Studies, Faculty of Humanities, University of Oulu, Oulu, Finland
| | - Anna-Kaisa Salmi
- Archaeology, History, Culture and Communication Studies, Faculty of Humanities, University of Oulu, Oulu, Finland
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12
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Keighley X, Bro‐Jørgensen MH, Ahlgren H, Szpak P, Ciucani MM, Sánchez Barreiro F, Howse L, Gotfredsen AB, Glykou A, Jordan P, Lidén K, Olsen MT. Predicting sample success for large-scale ancient DNA studies on marine mammals. Mol Ecol Resour 2021; 21:1149-1166. [PMID: 33463014 PMCID: PMC8248401 DOI: 10.1111/1755-0998.13331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 01/03/2021] [Accepted: 01/11/2021] [Indexed: 11/29/2022]
Abstract
In recent years, nonhuman ancient DNA studies have begun to focus on larger sample sizes and whole genomes, offering the potential to reveal exciting and hitherto unknown answers to ongoing biological and archaeological questions. However, one major limitation to such studies is the substantial financial and time investments still required during sample screening, due to uncertainty regarding successful sample selection. This study investigates the effect of a wide range of sample properties including latitude, sample age, skeletal element, collagen preservation, and context on endogenous content and DNA damage profiles for 317 ancient and historic pinniped samples collected from across the North Atlantic and surrounding regions. Using generalised linear and mixed-effect models, we found that a range of factors affected DNA preservation within each of the species under consideration. The most important findings were that endogenous content varied significantly within species according to context, the type of skeletal element, the collagen content and collection year. There also appears to be an effect of the sample's geographic origin, with samples from the Arctic generally showing higher endogenous content and lower damage rates. Both latitude and sample age were found to have significant relationships with damage levels, but only for walrus samples. Sex, ontogenetic age and extraction material preparation were not found to have any significant relationship with DNA preservation. Overall, skeletal element and sample context were found to be the most influential factors and should therefore be considered when selecting samples for large-scale ancient genome studies.
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Affiliation(s)
- Xénia Keighley
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen KDenmark
- Arctic Centre/Groningen Institute of ArchaeologyFaculty of ArtsUniversity of GroningenAS GroningenThe Netherlands
| | - Maiken Hemme Bro‐Jørgensen
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen KDenmark
- Archaeological Research LaboratoryDepartment of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Hans Ahlgren
- Archaeological Research LaboratoryDepartment of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Paul Szpak
- Department of AnthropologyTrent UniversityPeterboroughOntarioCanada
| | - Marta Maria Ciucani
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen KDenmark
| | | | - Lesley Howse
- Archaeology CentreUniversity of TorontoTorontoOntarioCanada
| | | | - Aikaterini Glykou
- Archaeological Research LaboratoryDepartment of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Peter Jordan
- Department of Archaeology and Ancient HistoryLund UniversityLundSweden
| | - Kerstin Lidén
- Archaeological Research LaboratoryDepartment of Archaeology and Classical StudiesStockholm UniversityStockholmSweden
| | - Morten Tange Olsen
- Section for Evolutionary GenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen KDenmark
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13
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Evans AR, Pollock TI, Cleuren SGC, Parker WMG, Richards HL, Garland KLS, Fitzgerald EMG, Wilson TE, Hocking DP, Adams JW. A universal power law for modelling the growth and form of teeth, claws, horns, thorns, beaks, and shells. BMC Biol 2021; 19:58. [PMID: 33781258 PMCID: PMC8008625 DOI: 10.1186/s12915-021-00990-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/22/2021] [Indexed: 11/29/2022] Open
Abstract
Background A major goal of evolutionary developmental biology is to discover general models and mechanisms that create the phenotypes of organisms. However, universal models of such fundamental growth and form are rare, presumably due to the limited number of physical laws and biological processes that influence growth. One such model is the logarithmic spiral, which has been purported to explain the growth of biological structures such as teeth, claws, horns, and beaks. However, the logarithmic spiral only describes the path of the structure through space, and cannot generate these shapes. Results Here we show a new universal model based on a power law between the radius of the structure and its length, which generates a shape called a ‘power cone’. We describe the underlying ‘power cascade’ model that explains the extreme diversity of tooth shapes in vertebrates, including humans, mammoths, sabre-toothed cats, tyrannosaurs and giant megalodon sharks. This model can be used to predict the age of mammals with ever-growing teeth, including elephants and rodents. We view this as the third general model of tooth development, along with the patterning cascade model for cusp number and spacing, and the inhibitory cascade model that predicts relative tooth size. Beyond the dentition, this new model also describes the growth of claws, horns, antlers and beaks of vertebrates, as well as the fangs and shells of invertebrates, and thorns and prickles of plants. Conclusions The power cone is generated when the radial power growth rate is unequal to the length power growth rate. The power cascade model operates independently of the logarithmic spiral and is present throughout diverse biological systems. The power cascade provides a mechanistic basis for the generation of these pointed structures across the tree of life. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-00990-w.
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Affiliation(s)
- Alistair R Evans
- School of Biological Sciences, Monash University, Melbourne, Victoria, 3800, Australia. .,Geosciences, Museums Victoria, Melbourne, Victoria, 3001, Australia.
| | - Tahlia I Pollock
- School of Biological Sciences, Monash University, Melbourne, Victoria, 3800, Australia
| | - Silke G C Cleuren
- School of Biological Sciences, Monash University, Melbourne, Victoria, 3800, Australia
| | - William M G Parker
- School of Biological Sciences, Monash University, Melbourne, Victoria, 3800, Australia
| | - Hazel L Richards
- School of Biological Sciences, Monash University, Melbourne, Victoria, 3800, Australia
| | - Kathleen L S Garland
- School of Biological Sciences, Monash University, Melbourne, Victoria, 3800, Australia
| | - Erich M G Fitzgerald
- School of Biological Sciences, Monash University, Melbourne, Victoria, 3800, Australia.,Geosciences, Museums Victoria, Melbourne, Victoria, 3001, Australia
| | - Tim E Wilson
- School of Mathematical Sciences, Monash University, Melbourne, Victoria, 3800, Australia
| | - David P Hocking
- School of Biological Sciences, Monash University, Melbourne, Victoria, 3800, Australia.,Geosciences, Museums Victoria, Melbourne, Victoria, 3001, Australia
| | - Justin W Adams
- Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, 3800, Australia
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14
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Pelletier M, Kotiaho A, Niinimäki S, Salmi AK. Identifying early stages of reindeer domestication in the archaeological record: a 3D morphological investigation on forelimb bones of modern populations from Fennoscandia. ARCHAEOLOGICAL AND ANTHROPOLOGICAL SCIENCES 2020; 12:169. [PMID: 32704330 PMCID: PMC7366605 DOI: 10.1007/s12520-020-01123-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
Reindeer herding probably developed during the Late Iron Age onwards and is still an important part of the subsistence and culture of many peoples in northern Eurasia. However, despite the importance of this husbandry in the history of these Arctic people, the period and place of the origin as well as the spread of domestic reindeer is still highly debated. Besides the existence of different breeding methods in these territories, identifying domesticated individuals in the archaeological record is complicated because reindeers are considered to still be in the early phases of the domestication process. Indeed, the traditional morphological markers used in zooarchaeology to decipher the domestication syndrome are hardly perceptible in these early stages. In this work, we propose solutions for identifying domestic reindeer bones using 3D geometric morphometrics on isolated elements from the long bones of the forelimb (i.e. humerus, radio-ulna and metacarpal). These bones are important to understand both the feeding behaviour and the mobility of reindeer, and the potential effect of load-carrying or draught in the case of domestic reindeer. We analysed 123 modern specimens from Fennoscandia, including the two interbreeding subspecies currently present in these territories: mountain reindeer (Rangifer tarandus tarandus) and forest reindeer (R.t. fennicus); and where the sex and the lifestyle were known (i.e. free-ranging, racing or draught and captive individuals). A good level of discrimination between the size and shape variables of the bones of the forelimb was found among both subspecies and sexes. Moreover, individuals bred in captivity had smaller bone elements and a thinner and more slender morphology than free-ranging individuals. This demonstrates that the long bones of the forelimb can provide information on changes in feeding and locomotor behaviour prompted by the domestication process, like control and/or reduction of mobility and food of individual reindeer by humans. This also demonstrates that analysis in 3D geometric morphometrics is useful in detecting reindeer incipient domestication markers. Our results can be used by archaeologists to trace the early stages of domestication from fossil reindeer remains, and aid in reconstructing the socio-economic changes of past Arctic populations over time.
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Affiliation(s)
- Maxime Pelletier
- Archaeology, History, Culture and Communication Studies, Faculty of Humanities, University of Oulu, Oulu, Finland
| | - Antti Kotiaho
- Department of Radiology, Oulu University Hospital, Oulu, Finland
| | - Sirpa Niinimäki
- Archaeology, History, Culture and Communication Studies, Faculty of Humanities, University of Oulu, Oulu, Finland
| | - Anna-Kaisa Salmi
- Archaeology, History, Culture and Communication Studies, Faculty of Humanities, University of Oulu, Oulu, Finland
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15
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Laakkonen J, Jernvall J. Muscles of Mastication and the Temporo-Mandibular Joint of the Saimaa (Pusa hispida saimensis) and Baltic (Pusa hispida botnica) Ringed Seals. ANN ZOOL FENN 2020. [DOI: 10.5735/086.057.0103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Juha Laakkonen
- Division of Veterinary Anatomy and Developmental Biology, Department of Veterinary Biosciences, Faculty of Veterinary Medicine, P.O. Box 66, FI-00014 University of Helsinki, Finland
| | - Jukka Jernvall
- Institute of Biotechnology, P.O. Box 56, FI-00014 University of Helsinki, Finland
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16
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Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization. Nat Commun 2019; 10:5560. [PMID: 31804475 PMCID: PMC6895188 DOI: 10.1038/s41467-019-13405-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 11/07/2019] [Indexed: 01/02/2023] Open
Abstract
Ecomorphological studies evaluating the impact of environmental and biological factors on the brain have so far focused on morphology or size measurements, and the ecological relevance of potential multi-level variations in brain architecture remains unclear in vertebrates. Here, we exploit the extraordinary ecomorphological diversity of squamates to assess brain phenotypic diversification with respect to locomotor specialization, by integrating single-cell distribution and transcriptomic data along with geometric morphometric, phylogenetic, and volumetric analysis of high-definition 3D models. We reveal significant changes in cerebellar shape and size as well as alternative spatial layouts of cortical neurons and dynamic gene expression that all correlate with locomotor behaviours. These findings show that locomotor mode is a strong predictor of cerebellar structure and pattern, suggesting that major behavioural transitions in squamates are evolutionarily correlated with mosaic brain changes. Furthermore, our study amplifies the concept of ‘cerebrotype’, initially proposed for vertebrate brain proportions, towards additional shape characters. The cerebellum is critical in sensory-motor control and is structurally diverse across vertebrates. Here, the authors investigate the evolutionary relationship between locomotory mode and cerebellum architecture across squamates by integrating study of gene expression, cell distribution, and 3D morphology.
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Hanot P, Herrel A, Guintard C, Cornette R. Unravelling the hybrid vigor in domestic equids: the effect of hybridization on bone shape variation and covariation. BMC Evol Biol 2019; 19:188. [PMID: 31615394 PMCID: PMC6794909 DOI: 10.1186/s12862-019-1520-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 09/26/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Hybridization has been widely practiced in plant and animal breeding as a means to enhance the quality and fitness of the organisms. In domestic equids, this hybrid vigor takes the form of improved physical and physiological characteristics, notably for strength or endurance. Because the offspring of horse and donkey is generally sterile, this widely recognized vigor is expressed in the first generation (F1). However, in the absence of recombination between the two parental genomes, F1 hybrids can be expected to be phenotypically intermediate between their parents which could potentially restrict the possibilities of an increase in overall fitness. In this study, we examine the morphology of the main limb bones of domestic horses, donkeys and their hybrids to investigate the phenotypic impact of hybridization on the locomotor system. We explore bone shape variation and covariation to gain insights into the morphological and functional expressions of the hybrid vigor commonly described in domestic equids. RESULTS Our data reveal the occurrence of transgressive effects on several bones in the F1 generation. The patterns of morphological integration further demonstrate that the developmental processes producing covariation are not disrupted by hybridization, contrary to functional ones. CONCLUSIONS These results suggest that an increase in overall fitness could be related to more flexibility in shape change in hybrids, except for the main forelimb long bones of which the morphology is strongly driven by muscle interactions. More broadly, this study illustrates the interest of investigating not only bone shape variation but also underlying processes, in order to contribute to better understanding how developmental and functional mechanisms are affected by hybridization.
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Affiliation(s)
- Pauline Hanot
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745, Jena, Germany.
| | - Anthony Herrel
- UMR 7179 " Mécanismes Adaptatifs et Évolution " (CNRS, MNHN), Muséum national d'Histoire naturelle, Sorbonne Universités, 57 rue Cuvier CP 55, 75005, Paris, France
| | - Claude Guintard
- Unité d'Anatomie Comparée, Ecole Nationale Vétérinaire de l'Agroalimentaire et de l'Alimentation, Nantes Atlantique - ONIRIS, cedex 03, route de Gachet, CS 40706, 44307, Nantes, France
- Groupe d'Études Remodelage osseux et bioMatériaux (GEROM), Université d'Angers, Unité INSERM 922, LHEA/IRIS-IBS, CHU d'Angers, 4 rue Larrey, Angers, France
| | - Raphaël Cornette
- UMR 7205 « Institut de Systématique, Évolution, Biodiversité » (CNRS, MNHN, UPMC, EPHE), Muséum national d'Histoire naturelle, Sorbonne Universités, 45 rue Buffon, 75005, Paris, France
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18
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Kierdorf U, Olsen MT, Kahle P, Ludolphy C, Kierdorf H. Dental pulp exposure, periapical inflammation and suppurative osteomyelitis of the jaws in juvenile Baltic grey seals (Halichoerus grypus grypus) from the late 19th century. PLoS One 2019; 14:e0215401. [PMID: 30978237 PMCID: PMC6461278 DOI: 10.1371/journal.pone.0215401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 04/01/2019] [Indexed: 11/19/2022] Open
Abstract
The systematic analysis of museum collections can provide important insights into the dental and skeletal pathology of wild mammals. Here we present a previously unreported type of dental defect and related skull pathology in five juvenile Baltic grey seals that had been collected in the course of a seal culling program along the Danish coast in 1889 and 1890. All five skulls exhibited openings into the pulp cavities at the crown tips of all (four animals) or two (one animal) canines as well as several incisors and (in one animal) also some anterior premolars. The affected teeth showed wide pulp cavities and thin dentin. Pulp exposure had caused infection, inflammation, and finally necrosis of the pulp. As was evidenced by the extensive radiolucency around the roots of the affected teeth, the inflammation had extended from the pulp into the periapical space, leading to apical periodontitis with extensive bone resorption. Further spreading of the inflammation into the surrounding bone regions had then caused suppurative osteomyelitis of the jaws. The postcanine teeth of the pathological individuals typically had dentin of normal thickness and, except for one specimen, did not exhibit pulp exposure. The condition may have been caused by a late onset of secondary and tertiary dentin formation that led to pulp exposure in anterior teeth exposed to intense wear. Future investigations could address a possible genetic causation of the condition in the studied grey seals.
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Affiliation(s)
- Uwe Kierdorf
- Department of Biology, University of Hildesheim, Hildesheim, Germany
- * E-mail:
| | - Morten T. Olsen
- Natural History Museum of Denmark, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Patricia Kahle
- Department of Biology, University of Hildesheim, Hildesheim, Germany
| | | | - Horst Kierdorf
- Department of Biology, University of Hildesheim, Hildesheim, Germany
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