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Scherz MD, Schmidt R, Brown JL, Glos J, Lattenkamp EZ, Rakotomalala Z, Rakotoarison A, Rakotonindrina RT, Randriamalala O, Raselimanana AP, Rasolonjatovo SM, Ratsoavina FM, Razafindraibe JH, Glaw F, Vences M. Repeated divergence of amphibians and reptiles across an elevational gradient in northern Madagascar. Ecol Evol 2023; 13:e9914. [PMID: 36937068 PMCID: PMC10019947 DOI: 10.1002/ece3.9914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 02/22/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
How environmental factors shape patterns of biotic diversity in tropical ecosystems is an active field of research, but studies examining the possibility of ecological speciation in terrestrial tropical ecosystems are scarce. We use the isolated rainforest herpetofauna on the Montagne d'Ambre (Amber Mountain) massif in northern Madagascar as a model to explore elevational divergence at the level of populations and communities. Based on intensive sampling and DNA barcoding of amphibians and reptiles along a transect ranging from ca. 470-1470 m above sea level (a.s.l.), we assessed a main peak in species richness at an elevation of ca. 1000 m a.s.l. with 41 species. The proportion of local endemics was highest (about 1/3) at elevations >1100 m a.s.l. Two species of chameleons (Brookesia tuberculata, Calumma linotum) and two species of frogs (Mantidactylus bellyi, M. ambony) studied in depth by newly developed microsatellite markers showed genetic divergence up the slope of the mountain, some quite strong, others very weak, but in each case with genetic breaks between 1100 and 1270 m a.s.l. Genetic clusters were found in transect sections significantly differing in bioclimate and herpetological community composition. A decrease in body size was detected in several species with increasing elevation. The studied rainforest amphibians and reptiles show concordant population genetic differentiation across elevation along with morphological and niche differentiation. Whether this parapatric or microallopatric differentiation will suffice for the completion of speciation is, however, unclear, and available phylogeographic evidence rather suggests that a complex interplay between ecological and allopatric divergence processes is involved in generating the extraordinary species diversity of Madagascar's biota. Our study reveals concordant patterns of diversification among main elevational bands, but suggests that these adaptational processes are only part of the complex of processes leading to species formation, among which geographical isolation is probably also important.
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Affiliation(s)
- Mark D. Scherz
- Zoologisches InstitutTechnische Universität BraunschweigBraunschweigGermany
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagen ØDenmark
| | - Robin Schmidt
- Zoologisches InstitutTechnische Universität BraunschweigBraunschweigGermany
| | - Jason L. Brown
- School of Biological SciencesSouthern Illinois UniversityCarbondaleIllinoisUSA
| | - Julian Glos
- Institute of Cell and Systems BiologyUniversität HamburgHamburgGermany
| | - Ella Z. Lattenkamp
- Neurogenetics of Vocal Communication GroupMax Planck Institute for PsycholinguisticsNijmegenThe Netherlands
- Division of Neurobiology, Department of Biology IILudwig Maximilians University MunichMartinsriedGermany
| | | | - Andolalao Rakotoarison
- Mention Zoologie et Biodiversité AnimaleUniversité d'AntananarivoAntananarivoMadagascar
- School for International TrainingAntananarivoMadagascar
| | | | - Onja Randriamalala
- Mention Zoologie et Biodiversité AnimaleUniversité d'AntananarivoAntananarivoMadagascar
| | - Achille P. Raselimanana
- Mention Zoologie et Biodiversité AnimaleUniversité d'AntananarivoAntananarivoMadagascar
- Association VahatraAntananarivoMadagascar
| | - Safidy M. Rasolonjatovo
- Mention Zoologie et Biodiversité AnimaleUniversité d'AntananarivoAntananarivoMadagascar
- Association VahatraAntananarivoMadagascar
| | | | - Jary H. Razafindraibe
- Mention Zoologie et Biodiversité AnimaleUniversité d'AntananarivoAntananarivoMadagascar
| | - Frank Glaw
- Zoologische Staatssammlung München (ZSM‐SNSB)MunichGermany
| | - Miguel Vences
- Zoologisches InstitutTechnische Universität BraunschweigBraunschweigGermany
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Population diversification in the frog Mantidactylus bellyi on an isolated massif in northern Madagascar based on genetic, morphological, bioacoustic and ecological evidence. PLoS One 2022; 17:e0263764. [PMID: 35358210 PMCID: PMC8970393 DOI: 10.1371/journal.pone.0263764] [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: 03/13/2021] [Accepted: 01/26/2022] [Indexed: 11/19/2022] Open
Abstract
In the processes that give rise to new species, changes first occur at the population level. But with the continuous nature of the divergence process, change in biological properties delimiting the shift from “individuals of divergent populations” towards “individuals of distinct species”, as well as abiotic factors driving the change, remain largely ambivalent. Here we study diversification processes at the population level in a semi-aquatic frog, Mantidactylus (Brygoomantis) bellyi, across the diverse vegetation types of Montagne d’Ambre National Park (MANP), Madagascar. Genetic diversity was assessed with seven newly developed microsatellite markers as well as mitochondrial DNA sequences and concordance with patterns of ecological, morphological, and bioacoustic divergence evaluated. We found M. bellyi lacking mitochondrial differentiation within MANP, while microsatellite datasets partitioned them into three highly differentiated, geographically separated subpopulations (with indications for up to five subpopulations). The molecular grouping–primarily clustering individuals by geographic proximity–was coincident with differences in mean depth and width of waters, suggesting a possible role of fluvial characteristics in genetic exchange in this stream-breeding species. Genetic clustering not consistent with differences in call properties, except for dominant call frequencies under the two-subpopulations model. Morphological divergence was mostly consistent with the genetic clustering; subpopulations strongly differed by their snout-vent length, with individuals from high-elevation subpopulations smaller than those from populations below 1000 m above sea level. These results exemplify how mountains and environmental conditions might primarily shape genetic and morphological divergence in frog populations, without strongly affecting their calls.
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Contrasting environmental drivers of genetic and phenotypic divergence in an Andean poison frog (Epipedobates anthonyi). Heredity (Edinb) 2022; 128:33-44. [PMID: 34718332 PMCID: PMC8733028 DOI: 10.1038/s41437-021-00481-2] [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: 01/07/2021] [Revised: 10/17/2021] [Accepted: 10/18/2021] [Indexed: 01/03/2023] Open
Abstract
Phenotypic and genetic divergence are shaped by the homogenizing effects of gene flow and the differentiating processes of genetic drift and local adaptation. Herein, we examined the mechanisms that underlie phenotypic (size and color) and genetic divergence in 35 populations (535 individuals) of the poison frog Epipedobates anthonyi along four elevational gradients (0-1800 m asl) in the Ecuadorian Andes. We found phenotypic divergence in size and color despite relatively low genetic divergence at neutral microsatellite loci. Genetic and phenotypic divergence were both explained by landscape resistance between sites (isolation-by-resistance, IBR), likely due to a cold and dry mountain ridge between the northern and southern elevational transects that limits dispersal and separates two color morphs. Moreover, environmental differences among sites also explained genetic and phenotypic divergence, suggesting isolation-by-environment (IBE). When northern and southern transects were analyzed separately, genetic divergence was predicted either by distance (isolation-by-distance, IBD; northern) or environmental resistance between sites (IBR; southern). In contrast, phenotypic divergence was primarily explained by environmental differences among sites, supporting the IBE hypothesis. These results indicate that although distance and geographic barriers are important drivers of population divergence, environmental variation has a two-fold effect on population divergence. On the one hand, landscape resistance between sites reduces gene flow (IBR), while on the other hand, environmental differences among sites exert divergent selective pressures on phenotypic traits (IBE). Our work highlights the importance of studying both genetic and phenotypic divergence to better understand the processes of population divergence and speciation along ecological gradients.
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Wambulwa MC, Milne R, Wu Z, Spicer RA, Provan J, Luo Y, Zhu G, Wang W, Wang H, Gao L, Li D, Liu J. Spatiotemporal maintenance of flora in the Himalaya biodiversity hotspot: Current knowledge and future perspectives. Ecol Evol 2021; 11:10794-10812. [PMID: 34429882 PMCID: PMC8366862 DOI: 10.1002/ece3.7906] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 01/02/2023] Open
Abstract
Mountain ecosystems support a significant one-third of all terrestrial biodiversity, but our understanding of the spatiotemporal maintenance of this high biodiversity remains poor, or at best controversial. The Himalaya hosts a complex mountain ecosystem with high topographic and climatic heterogeneity and harbors one of the world's richest floras. The high species endemism, together with increasing anthropogenic threats, has qualified the Himalaya as one of the most significant global biodiversity hotspots. The topographic and climatic complexity of the Himalaya makes it an ideal natural laboratory for studying the mechanisms of floral exchange, diversification, and spatiotemporal distributions. Here, we review literature pertaining to the Himalaya in order to generate a concise synthesis of the origin, distribution, and climate change responses of the Himalayan flora. We found that the Himalaya supports a rich biodiversity and that the Hengduan Mountains supplied the majority of the Himalayan floral elements, which subsequently diversified from the late Miocene onward, to create today's relatively high endemicity in the Himalaya. Further, we uncover links between this Miocene diversification and the joint effect of geological and climatic upheavals in the Himalaya. There is marked variance regarding species dispersal, elevational gradients, and impact of climate change among plant species in the Himalaya, and our review highlights some of the general trends and recent advances on these aspects. Finally, we provide some recommendations for conservation planning and future research. Our work could be useful in guiding future research in this important ecosystem and will also provide new insights into the maintenance mechanisms underpinning other mountain systems.
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Affiliation(s)
- Moses C. Wambulwa
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Department of Life SciencesSchool of Pure and Applied SciencesSouth Eastern Kenya UniversityKituiKenya
| | - Richard Milne
- Institute of Molecular Plant SciencesSchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Zeng‐Yuan Wu
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Robert A. Spicer
- CAS Key Laboratory of Tropical Forest EcologyXishuangbanna Tropical Botanical GardenChinese Academy of SciencesXishuangbannaChina
- School of Environment, Earth and Ecosystem SciencesThe Open UniversityMilton KeynesUK
| | - Jim Provan
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Ya‐Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Guang‐Fu Zhu
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- University of the Chinese Academy of SciencesBeijingChina
- Kunming College of Life SciencesUniversity of Chinese Academy of SciencesKunmingChina
| | - Wan‐Ting Wang
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- University of the Chinese Academy of SciencesBeijingChina
- Kunming College of Life SciencesUniversity of Chinese Academy of SciencesKunmingChina
| | - Hong Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Lian‐Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - De‐Zhu Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Kunming College of Life SciencesUniversity of Chinese Academy of SciencesKunmingChina
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingChina
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García-Rodríguez A, Martínez PA, Oliveira BF, Velasco JA, Pyron RA, Costa GC. Amphibian Speciation Rates Support a General Role of Mountains as Biodiversity Pumps. Am Nat 2021; 198:E68-E79. [PMID: 34403310 DOI: 10.1086/715500] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractContinental mountain areas cover <15% of global land surface, yet these regions concentrate >80% of global terrestrial diversity. One prominent hypothesis to explain this pattern proposes that high mountain diversities could be explained by higher diversification rates in regions of high topographic complexity (HTC). While high speciation in mountains has been detected for particular clades and regions, the global extent to which lineages experience faster speciation in mountains remains unknown. Here we addressed this issue using amphibians as a model system (>7,000 species), and we found that families showing high speciation rates contain a high proportion of species distributed in mountains. Moreover, we found that lineages inhabiting areas of HTC speciate faster than lineages occupying areas that are topographically less complex. When comparing across regions, we identified the same pattern in five biogeographical realms where higher speciation rates are associated with higher levels of complex topography. Low-magnitude differences in speciation rates between some low and high complex topographies suggest that high mountain diversity is also affected by low extinction and/or high colonization rates. Nevertheless, our results bolster the importance of mountains as engines of speciation at different geographical scales and highlight their importance for the conservation of global biodiversity.
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Demari-Silva B, Laporta GZ, de Oliveira TMP, Sallum MAM. Evidence of Elevational Speciation in Kerteszia cruzii (Diptera: Culicidae) in the Ribeira Valley, São Paulo, Brazil. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.707642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Kerteszia cruzii [former Anopheles (Kerteszia) cruzii] is a bromeliad mosquito widespread in the Brazilian Atlantic rainforest. In South-eastern Brazil, it plays an important role in malaria transmission because it was infected with at least four Plasmodium species. There is robust evidence that Ke. cruzii is a species complex. We used single nucleotide polymorphisms (SNPs) from a nextRAD sequence (nextera-tagmented, reductively amplified DNA) to investigate the genetic structure of Ke. cruzii in the Ribeira Valley, South-eastern Brazil. Furthermore, we verified whether the genetic structure was associated with forest cover, elevation, slope, and vegetation physiognomy. Our results showed two distinct lineages in the studied region associated with elevation and isolation by distance. The first lineage included samples from coastal localities and the second comprised specimens from inland or mountain sites. At one sampling locality (Esteiro do Morro in Cananéia municipality), both lineages are sympatric. These results are in accordance with previously published data that showed elevated stratification in Ke. cruzii. However, Fst values did not indicate the existence of cryptic or sister species in Ke. cruzii in this region, we concluded that elevational speciation probably occurs, and we hypothesized that differences in population structure found might be associated with the distribution of bromeliad species.
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7
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Medina R, Wogan GOU, Bi K, Termignoni-García F, Bernal MH, Jaramillo-Correa JP, Wang IJ, Vázquez-Domínguez E. Phenotypic and genomic diversification with isolation by environment along elevational gradients in a neotropical treefrog. Mol Ecol 2021; 30:4062-4076. [PMID: 34160853 DOI: 10.1111/mec.16035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 01/03/2023]
Abstract
Understanding how geographic and environmental heterogeneity drive local patterns of genetic variation is a major goal of ecological genomics and a key question in evolutionary biology. The tropical Andes and inter-Andean valleys are shaped by markedly heterogeneous landscapes, where species experience strong selective processes. We examined genome-wide SNP data together with behavioural and ecological traits (mating calls and body size) known to contribute to genetic isolation in anurans in the banana tree-dwelling frog, Boana platanera, distributed across an environmental gradient in Central Colombia (northern South America). Here, we analysed the relationships between environmentally (temperature and precipitation) associated genetic and phenotypic differentiation and the potential drivers of isolation by environment along an elevation gradient. We identified candidate SNPs associated with temperature and body size, which follow a clinal pattern of genome-wide differentiation tightly coupled with phenotypic variation: as elevation increases, B. platanera exhibits larger body size and longer call duration with more pulses but lower pulse rate and frequency. Thus, the environmental landscape has rendered a scenario where isolation by environment and candidate loci show concordance with phenotypic divergence in this tropical frog along an elevation gradient in the Colombian Andes. Our study sets the basis for evaluating the role of temperature in the genetic structure and local adaptation in tropical treefrogs and its putative effect on life cycle (embryos, tadpoles, adults) along elevation gradients.
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Affiliation(s)
- Ricardo Medina
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México.,Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México.,Grupo de Herpetología, Eco-Fisiología & Etología, Departamento de Biología, Universidad del Tolima, Altos de Santa Helena, Ibagué, Colombia
| | - Guinevere O U Wogan
- Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley, California, USA.,Department of Integrative Biology, Oklahoma State University, Oklahoma, USA
| | - Ke Bi
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA.,Computational Genomics Resource Laboratory (CGRL, California Institute for Quantitative Biosciences (QB3, University of California, Berkeley, California, USA
| | - Flavia Termignoni-García
- Department of Organismic and Evolutionary Biology (OEB, Harvard University, Cambridge, Massachusetts, USA
| | - Manuel Hernando Bernal
- Grupo de Herpetología, Eco-Fisiología & Etología, Departamento de Biología, Universidad del Tolima, Altos de Santa Helena, Ibagué, Colombia
| | - Juan P Jaramillo-Correa
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley, California, USA
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, México
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Abstract
Understanding the genetic mechanisms underlying particular adaptations/phenotypes of organisms is one of the core issues of evolutionary biology. The use of genomic data has greatly advanced our understandings on this issue, as well as other aspects of evolutionary biology, including molecular adaptation, speciation, and even conservation of endangered species. Despite the well-recognized advantages, usages of genomic data are still limited to non-mammal vertebrate groups, partly due to the difficulties in assembling large or highly heterozygous genomes. Although this is particularly the case for amphibians, nonetheless, several comparative and population genomic analyses have shed lights into the speciation and adaptation processes of amphibians in a complex landscape, giving a promising hope for a wider application of genomics in the previously believed challenging groups of organisms. At the same time, these pioneer studies also allow us to realize numerous challenges in studying the molecular adaptations and/or phenotypic evolutionary mechanisms of amphibians. In this review, we first summarize the recent progresses in the study of adaptive evolution of amphibians based on genomic data, and then we give perspectives regarding how to effectively identify key pathways underlying the evolution of complex traits in the genomic era, as well as directions for future research.
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Affiliation(s)
- Yan-Bo Sun
- Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, Yunnan 650091, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
| | - Yi Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Kai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, Oklahoma 73072, USA
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Density Dependence and Adult Survival Drive Dynamics in Two High Elevation Amphibian Populations. DIVERSITY 2020. [DOI: 10.3390/d12120478] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Amphibian conservation has progressed from the identification of declines to mitigation, but efforts are hampered by the lack of nuanced information about the effects of environmental characteristics and stressors on mechanistic processes of population regulation. Challenges include a paucity of long-term data and scant information about the relative roles of extrinsic (e.g., weather) and intrinsic (e.g., density dependence) factors. We used a Bayesian formulation of an open population capture-recapture model and >30 years of data to examine intrinsic and extrinsic factors regulating two adult boreal chorus frogs (Pseudacris maculata) populations. We modelled population growth rate and apparent survival directly, assessed their temporal variability, and derived estimates of recruitment. Populations were relatively stable (geometric mean population growth rate >1) and regulated by negative density dependence (i.e., higher population sizes reduced population growth rate). In the smaller population, density dependence also acted on adult survival. In the larger population, higher population growth was associated with warmer autumns. Survival estimates ranged from 0.30–0.87, per-capita recruitment was <1 in most years, and mean seniority probability was >0.50, suggesting adult survival is more important to population growth than recruitment. Our analysis indicates density dependence is a primary driver of population dynamics for P. maculata adults.
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Peng JC, Ma XG, Wang YH, Sun H. New insights into the evolutionary history of Megacodon: Evidence from a newly discovered species. PLANT DIVERSITY 2020; 42:198-208. [PMID: 32695953 PMCID: PMC7361429 DOI: 10.1016/j.pld.2020.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
Megacodon is an ideal genus to study speciation and ecological adaptation in the Sino-Himalayan region. The genus contains two species distributed at different elevations and in two separate areas. However, studies of this genus have long been impeded by a lack of fieldwork on one of its species, Megacodon venosus. In this study, we collected specimens of two Megacodon species and found an extraordinary new species of Megacodon in Lushui county of north-west Yunnan province, which we have since named Megacodon lushuiensis. We propose new species based on both morphological and molecular evidence. The finding of this new species emphasized the importance of ecological divergence in the divergence of Megacodon stylophorus and its parapatric low-elevation Megacodon species. To identify genetic determinants that underlie adaptations to different elevations, we characterized transcriptomes of the new species M. lushuiensis, which is distributed at low elevations, and M. stylophorus, which is distributed at high elevations. Comparative transcriptome analysis identified 8926 orthogroups containing single-copy genes, and 370 orthogroups containing significantly positively selected genes. The set of positively selected genes was enriched into 25 Gene Ontology terms, including "response to water deprivation", "response to osmotic stress", and "cellular response to external stimulus". Our results provide new insights into how ecological adaptation and speciation occurred in Megacodon and highlight the role of heterogeneous habitats in the speciation of plants in the Sino-Himalayan region.
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Affiliation(s)
- Jun-Chu Peng
- School of Life Sciences, Yunnan University, Kunming 650091, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang-Guang Ma
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yue-Hua Wang
- School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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11
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Van Buskirk J, Jansen van Rensburg A. Relative importance of isolation‐by‐environment and other determinants of gene flow in an alpine amphibian. Evolution 2020; 74:962-978. [DOI: 10.1111/evo.13955] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/26/2020] [Accepted: 03/09/2020] [Indexed: 02/07/2023]
Affiliation(s)
- Josh Van Buskirk
- Department of Evolutionary Biology and Environmental StudiesUniversity of Zurich Zurich 8057 Switzerland
| | - Alexandra Jansen van Rensburg
- Department of Evolutionary Biology and Environmental StudiesUniversity of Zurich Zurich 8057 Switzerland
- School of Biological SciencesUniversity of Bristol Bristol BS8 1TQ United Kingdom
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12
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Origin of Elevational Replacements in a Clade of Nearly Flightless Birds: Most Diversity in Tropical Mountains Accumulates via Secondary Contact Following Allopatric Speciation. NEOTROPICAL DIVERSIFICATION: PATTERNS AND PROCESSES 2020. [DOI: 10.1007/978-3-030-31167-4_23] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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13
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Billerman SM, Jesmer BR, Watts AG, Schlichting PE, Fortin MJ, Funk WC, Hapeman P, Muths E, Murphy MA. Testing theoretical metapopulation conditions with genotypic data from Boreal Chorus Frogs (Pseudacris maculata). CAN J ZOOL 2019. [DOI: 10.1139/cjz-2018-0275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The metapopulation concept has far-reaching implications in ecology and conservation biology. Hanski’s criteria operationally define metapopulations, yet testing them is hindered by logistical and financial constraints inherent to the collection of long-term demographic data. Hence, ecologists and conservationists often assume metapopulation existence for dispersal-limited species that occupy patchy habitats. To advance understanding of metapopulation theory and improve conservation of metapopulations, we used population and landscape genetic tools to develop a methodological framework for evaluating Hanski’s criteria. We used genotypic data (11 microsatellite loci) from a purported metapopulation of Boreal Chorus Frogs (Pseudacris maculata (Agassiz, 1850)) in Colorado, U.S.A., to test Hanski’s four criteria. We found support for each criterion: (1) significant genetic differentiation between wetlands, suggesting distinct breeding populations; (2) wetlands had small effective population sizes and recent bottlenecks, suggesting populations do not experience long-term persistence; (3) population graphs provided evidence of gene flow between patches, indicating potential for recolonization; and (4) multiscale bottleneck analyses suggest asynchrony, indicating that simultaneous extinction of all populations was unlikely. Our methodological framework provides a logistically and financially feasible alternative to long-term demographic data for identifying amphibian metapopulations.
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Affiliation(s)
- Shawn M. Billerman
- Program in Ecology, Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, U.S.A
- University of Wyoming, Laramie, WY 82071, U.S.A
| | - Brett R. Jesmer
- Program in Ecology, Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, U.S.A
- University of Wyoming, Laramie, WY 82071, U.S.A
| | - Alexander G. Watts
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
- Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, ON M5B 1T8, Canada
| | - Peter E. Schlichting
- Department of Natural Resources Management, Texas Tech University, Lubbock, TX 79409, U.S.A
- Arizona State University – Polytechnic Campus, Mesa, AZ 85212, U.S.A
| | - Marie-Josée Fortin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - W. Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - Paul Hapeman
- Department of Biology, Central Connecticut State University, New Britain, CT 06053, U.S.A
| | - Erin Muths
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO 80526, U.S.A
| | - Melanie A. Murphy
- University of Wyoming, Laramie, WY 82071, U.S.A
- Department of Ecosystem Science and Management, University of Wyoming, Laramie, WY 82071, U.S.A
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14
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Wollenberg Valero KC, Marshall JC, Bastiaans E, Caccone A, Camargo A, Morando M, Niemiller ML, Pabijan M, Russello MA, Sinervo B, Werneck FP, Sites JW, Wiens JJ, Steinfartz S. Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians. Genes (Basel) 2019; 10:genes10090646. [PMID: 31455040 PMCID: PMC6769790 DOI: 10.3390/genes10090646] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/21/2019] [Accepted: 08/05/2019] [Indexed: 12/22/2022] Open
Abstract
In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in these groups. This study then reviews the research on different aspects of speciation in reptiles and amphibians, including biogeography and climatic niches, ecological speciation, the relationship between speciation rates and phenotypic traits, and genetics and genomics. Further, several case studies of speciation in reptiles and amphibians that exemplify many of these themes are discussed. These include studies of integrative taxonomy and biogeography in South American lizards, ecological speciation in European salamanders, speciation and phenotypic evolution in frogs and lizards. The final case study combines genomics and biogeography in tortoises. The field of amphibian and reptile speciation research has steadily moved forward from the assessment of geographic and ecological aspects, to incorporating other dimensions of speciation, such as genetic mechanisms and evolutionary forces. A higher degree of integration among all these dimensions emerges as a goal for future research.
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Affiliation(s)
| | - Jonathon C Marshall
- Department of Zoology, Weber State University, 1415 Edvalson Street, Dept. 2505, Ogden, UT 84401, USA
| | - Elizabeth Bastiaans
- Department of Biology, State University of New York, College at Oneonta, Oneonta, NY 13820, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Arley Camargo
- Centro Universitario de Rivera, Universidad de la República, Ituzaingó 667, Rivera 40000, Uruguay
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC, CENPAT-CONICET) Bv. Brown 2915, Puerto Madryn U9120ACD, Argentina
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Maciej Pabijan
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387 Kraków, Poland
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC V1V 1V7, Canada
| | - Barry Sinervo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Coastal Biology Building, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Fernanda P Werneck
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus 69060-000, Brazil
| | - Jack W Sites
- Department of Biological and Marine Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Sebastian Steinfartz
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany
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15
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Norman JA, Christidis L, Schodde R. Ecological and evolutionary diversification in the Australo-Papuan scrubwrens (Sericornis) and mouse-warblers (Crateroscelis), with a revision of the subfamily Sericornithinae (Aves: Passeriformes: Acanthizidae). ORG DIVERS EVOL 2018. [DOI: 10.1007/s13127-018-0364-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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16
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Advancing Understanding of Amphibian Evolution, Ecology, Behavior, and Conservation with Massively Parallel Sequencing. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_61] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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17
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Gutiérrez-Rodríguez J, Gonçalves J, Civantos E, Martínez-Solano I. Comparative landscape genetics of pond-breeding amphibians in Mediterranean temporal wetlands: The positive role of structural heterogeneity in promoting gene flow. Mol Ecol 2017; 26:5407-5420. [PMID: 28752597 DOI: 10.1111/mec.14272] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 06/12/2017] [Accepted: 07/12/2017] [Indexed: 01/14/2023]
Abstract
Comparative landscape genetics studies can provide key information to implement cost-effective conservation measures favouring a broad set of taxa. These studies are scarce, particularly in Mediterranean areas, which include diverse but threatened biological communities. Here, we focus on Mediterranean wetlands in central Iberia and perform a multi-level, comparative study of two endemic pond-breeding amphibians, a salamander (Pleurodeles waltl) and a toad (Pelobates cultripes). We genotyped 411 salamanders from 20 populations and 306 toads from 16 populations at 18 and 16 microsatellite loci, respectively, and identified major factors associated with population connectivity through the analysis of three sets of variables potentially affecting gene flow at increasingly finer levels of spatial resolution. Topographic, land use/cover, and remotely sensed vegetation/moisture indices were used to derive optimized resistance surfaces for the two species. We found contrasting patterns of genetic structure, with stronger, finer scale genetic differentiation in Pleurodeles waltl, and notable differences in the role of fine-scale patterns of heterogeneity in vegetation cover and water content in shaping patterns of regional genetic structure in the two species. Overall, our results suggest a positive role of structural heterogeneity in population connectivity in pond-breeding amphibians, with habitat patches of Mediterranean scrubland and open oak woodlands ("dehesas") facilitating gene flow. Our study highlights the usefulness of remotely sensed continuous variables of land cover, vegetation and water content (e.g., NDVI, NDMI) in conservation-oriented studies aimed at identifying major drivers of population connectivity.
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Affiliation(s)
| | - João Gonçalves
- Centro de Investigacão em Biodiversidade e Recursos Genéticos da Universidade do Porto, CIBIO/InBIO, Vairão, Portugal
| | - Emilio Civantos
- Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain.,Centro de Investigacão em Biodiversidade e Recursos Genéticos da Universidade do Porto, CIBIO/InBIO, Vairão, Portugal
| | - Iñigo Martínez-Solano
- Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain.,Centro de Investigacão em Biodiversidade e Recursos Genéticos da Universidade do Porto, CIBIO/InBIO, Vairão, Portugal.,Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM), Ciudad Real, Spain.,Ecology, Evolution and Development Group, Department of Wetland Ecology, Doñana Biological Station, CSIC, Seville, Spain
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18
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Muths E, Scherer R, Amburgey S, Matthews T, Spencer A, Corn P. First estimates of the probability of survival in a small-bodied, high-elevation frog (Boreal Chorus Frog, Pseudacris maculata), or how historical data can be useful. CAN J ZOOL 2016. [DOI: 10.1139/cjz-2016-0024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In an era of shrinking budgets yet increasing demands for conservation, the value of existing (i.e., historical) data are elevated. Lengthy time series on common, or previously common, species are particularly valuable and may be available only through the use of historical information. We provide first estimates of the probability of survival and longevity (0.67–0.79 and 5–7 years, respectively) for a subalpine population of a small-bodied, ostensibly common amphibian, the Boreal Chorus Frog (Pseudacris maculata (Agassiz, 1850)), using historical data and contemporary, hypothesis-driven information–theoretic analyses. We also test a priori hypotheses about the effects of color morph (as suggested by early reports) and of drought (as suggested by recent climate predictions) on survival. Using robust mark–recapture models, we find some support for early hypotheses regarding the effect of color on survival, but we find no effect of drought. The congruence between early findings and our analyses highlights the usefulness of historical information in providing raw data for contemporary analyses and context for conservation and management decisions.
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Affiliation(s)
- E. Muths
- U.S. Geological Survey, Fort Collins Science Center, 2150 Centre Avenue, Building C, Fort Collins, CO 80526, USA
| | - R.D. Scherer
- Conservation Science Partners, 501 Old Town Square, Fort Collins, CO 80524 USA
| | - S.M. Amburgey
- Department of Ecosystem Science and Management, Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA 16802, USA
| | - T. Matthews
- 1414 Nunn Creek Court, Fort Collins, CO 80526, USA
| | - A.W. Spencer
- Fort Lewis College, Department of Biology, Durango, CO 81301, USA
| | - P.S. Corn
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Aldo Leopold Wilderness Research Institute, Missoula, MT 59801, USA
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19
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McClure M, Elias M. Unravelling the role of host plant expansion in the diversification of a Neotropical butterfly genus. BMC Evol Biol 2016; 16:128. [PMID: 27306900 PMCID: PMC4910189 DOI: 10.1186/s12862-016-0701-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/07/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding the processes underlying diversification is a central question in evolutionary biology. For butterflies, access to new host plants provides opportunities for adaptive speciation. On the one hand, locally abundant host species can generate ecologically significant selection pressure. But a diversity of host plant species within the geographic range of each population and/or species might also eliminate any advantage conferred by specialization. This paper focuses on four Melinaea species, which are oligophagous on the family Solanaceae: M. menophilus, M. satevis, M. marsaeus, and finally, M. mothone. We examined both female preference and larval performance on two host plant species that commonly occur in this butterfly's native range, Juanulloa parasitica and Trianaea speciosa, to determine whether the different Melinaea species show evidence of local adaptation. RESULT In choice experiments, M. mothone females used both host plants for oviposition, whereas all other species used J. parasitica almost exclusively. In no choice experiment, M. mothone was the only species that readily accepted T. speciosa as a larval host plant. Larval survival was highest on J. parasitica (82.0 % vs. 60.9 %) and development took longer on T. speciosa (14.12 days vs. 13.35 days), except for M. mothone, which did equally well on both host plants. For all species, average pupal weight was highest on J. parasitica (450.66 mg vs. 420.01 mg), although this difference was least apparent in M. mothone. CONCLUSION We did not find that coexisting species of Melinaea partition host plant resources as expected if speciation is primarily driven by host plant divergence. Although M. mothone shows evidence of local adaptation to a novel host plant, T. speciosa, which co-occurs, it does not preferentially lay more eggs on or perform better on this host plant than on host plants used by other Melinaea species and not present in its distributional range. It is likely that diversification in this genus is driven by co-occurring Müllerian mimics and the resulting predation pressure, although this is also likely made possible by greater niche diversity as a consequence of plasticity for potential hosts.
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Affiliation(s)
- Melanie McClure
- Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum National d'Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier, CP50, F-75005, Paris, France.
| | - Marianne Elias
- Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum National d'Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier, CP50, F-75005, Paris, France
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20
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Ujiié Y, Ishitani Y. Evolution of a Planktonic Foraminifer during Environmental Changes in the Tropical Oceans. PLoS One 2016; 11:e0148847. [PMID: 26886349 PMCID: PMC4757448 DOI: 10.1371/journal.pone.0148847] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/25/2016] [Indexed: 11/18/2022] Open
Abstract
Ecological adaptation to environmental changes is a strong driver of evolution, enabling speciation of pelagic plankton in the open ocean without the presence of effective physical barriers to gene flow. The tropical ocean environment, which plays an important role in shaping marine biodiversity, has drastically and frequently changed since the Pliocene. Nevertheless, the evolutionary history of tropical pelagic plankton has been poorly understood, as phylogeographic investigations are still in the developing state and paleontological approaches are insufficient to obtain a sequential record from the deep-sea sediments. The planktonic foraminifer Pulleniatina obliquiloculata is widely distributed in the tropical area throughout the world’s oceans, and its phylogeography is well established. It is thus one of the best candidates to examine how past environmental changes may have shifted the spatial distribution and affected the diversification of tropical pelagic plankton. Such an examination requires the divergence history of the planktonic foraminifers, yet the gene marker (partial small subunit (SSU) rDNA) previously used for phylogeographic studies was not powerful enough to achieve a high accuracy in estimating the divergence times. The present study focuses on improving the precision of divergence time estimates for the splits between sibling species (genetic types) of planktonic foraminifers by increasing the number of genes as well as the number of nucleotide bases used for molecular clock estimates. We have amplified the entire coding regions of two ribosomal RNA genes (SSU rDNA and large subunit (LSU) rDNA) of three genetic types of P. obliquiloculata and two closely related species for the first time and applied them to the Bayesian relaxed clock method. The comparison of the credible intervals of the four datasets consisting either of sequences of the partial SSU rDNA, the complete SSU rDNA, LSU rDNA, or a combination of both genes (SSU+LSU) clearly demonstrated that the two-gene dataset improved the accuracy of divergence time estimates. The P. obliquiloculata lineage diverged twice, first at the end of the Pliocene (3.1 Ma) and again in the middle Pleistocene (1.4 Ma). Both timings coincided with the environmental changes, which indirectly involved geographic separation of populations. The habitat of P. obliquiloculata was expanded toward the higher latitudinal zones during the stable warm periods and subsequently placed on the steep environmental gradients following the global cooling. Different environmental conditions in the stable warm tropics and unstable higher latitudes may have triggered ecological divergence among the populations, leading to adaptive differentiation and eventually speciation. A comprehensive analysis of divergence time estimates combined with phylogeography enabled us to reveal the evolutionary history of the pelagic plankton and to find the potential paleoenvironmental events, which could have changed their biogeography and ecology.
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Affiliation(s)
- Yurika Ujiié
- Department of Biology, Shinshu University, Matsumoto, Nagano, Japan
- * E-mail:
| | - Yoshiyuki Ishitani
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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