1
|
de Almeida Borghezan E, da Silva Pires TH, Zuanon J, Sugiura H, Kohshima S, Kishida T. Unstable environmental conditions constrain the fine-tune between opsin sensitivity and underwater light in an Amazon forest stream fish. J Evol Biol 2024; 37:212-224. [PMID: 38262627 DOI: 10.1093/jeb/voae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 11/07/2023] [Accepted: 01/07/2024] [Indexed: 01/25/2024]
Abstract
Visual adaptations can stem from variations in amino acid composition, chromophore utilization, and differential opsin gene expression levels, enabling individuals to adjust their light sensitivity to environmental lighting conditions. In stable environments, adaptations often involve amino acid substitutions, whereas in unstable conditions, differential gene expression may be a more relevant mechanism. Amazon forest streams present diverse underwater lighting conditions and experience short-term water colour fluctuations. In these environments, it is less likely for genetic and amino acid sequences to undergo modifications that tailor opsin proteins to the prevailing lighting conditions, particularly in species having several copies of the same gene. The sailfin tetra, Crenuchus spilurus, inhabits black and clear water Amazon forest streams. The long-wavelength sensitivity (LWS) is an important component for foraging and courtship. Here, we investigated LWS opsin genes in the sailfin tetra. Three copies of LWS1 and two copies of LWS2 genes were found. The maximum absorbance wavelength (λmax) estimated from the amino acid sequences of LWS1 genes exhibited variation among the different copies. In contrast, the copies of LWS2 genes showed identical expected λmax values. Although the amino acid positions affecting λmax varied among LWS genes, they remained consistent among populations living in different water colours. The relative expression levels of LWS genes differed between gene copies. While not formally tested, our results suggest that in fluctuating environments, visual adaptations may primarily stem from alterations in gene expression profiles and/or chromophore usage rather than precise genetic tuning of protein light sensitivity to environmental lighting conditions.
Collapse
Affiliation(s)
- Elio de Almeida Borghezan
- Wildlife Research Center of the Kyoto University, Kyoto, Japan
- National Institute for Amazonian Research, Manaus, Brazil
| | | | - Jansen Zuanon
- National Institute for Amazonian Research, Manaus, Brazil
| | - Hideki Sugiura
- Wildlife Research Center of the Kyoto University, Kyoto, Japan
| | - Shiro Kohshima
- Wildlife Research Center of the Kyoto University, Kyoto, Japan
| | - Takushi Kishida
- Wildlife Research Center of the Kyoto University, Kyoto, Japan
- College of Bioresource Sciences, Nihon University, Fujisawa, Japan
| |
Collapse
|
2
|
Sylvain FÉ, Bouslama S, Holland A, Leroux N, Mercier PL, Val AL, Derome N. Bacterioplankton Communities in Dissolved Organic Carbon-Rich Amazonian Black Water. Microbiol Spectr 2023; 11:e0479322. [PMID: 37199657 PMCID: PMC10269884 DOI: 10.1128/spectrum.04793-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/04/2023] [Indexed: 05/19/2023] Open
Abstract
The Amazon River basin sustains dramatic hydrochemical gradients defined by three water types: white, clear, and black waters. In black water, important loads of allochthonous humic dissolved organic matter (DOM) result from the bacterioplankton degradation of plant lignin. However, the bacterial taxa involved in this process remain unknown, since Amazonian bacterioplankton has been poorly studied. Its characterization could lead to a better understanding of the carbon cycle in one of the Earth's most productive hydrological systems. Our study characterized the taxonomic structure and functions of Amazonian bacterioplankton to better understand the interplay between this community and humic DOM. We conducted a field sampling campaign comprising 15 sites distributed across the three main Amazonian water types (representing a gradient of humic DOM), and a 16S rRNA metabarcoding analysis based on bacterioplankton DNA and RNA extracts. Bacterioplankton functions were inferred using 16S rRNA data in combination with a tailored functional database from 90 Amazonian basin shotgun metagenomes from the literature. We discovered that the relative abundances of fluorescent DOM fractions (humic-, fulvic-, and protein-like) were major drivers of bacterioplankton structure. We identified 36 genera for which the relative abundance was significantly correlated with humic DOM. The strongest correlations were found in the Polynucleobacter, Methylobacterium, and Acinetobacter genera, three low abundant but omnipresent taxa that possessed several genes involved in the main steps of the β-aryl ether enzymatic degradation pathway of diaryl humic DOM residues. Overall, this study identified key taxa with DOM degradation genomic potential, the involvement of which in allochthonous Amazonian carbon transformation and sequestration merits further investigation. IMPORTANCE The Amazon basin discharge carries an important load of terrestrially derived dissolved organic matter (DOM) to the ocean. The bacterioplankton from this basin potentially plays important roles in transforming this allochthonous carbon, which has consequences on marine primary productivity and global carbon sequestration. However, the structure and function of Amazonian bacterioplanktonic communities remain poorly studied, and their interactions with DOM are unresolved. In this study, we (i) sampled bacterioplankton in all the main Amazon tributaries, (ii) combined information from the taxonomic structure and functional repertory of Amazonian bacterioplankton communities to understand their dynamics, (iii) identified the main physicochemical parameters shaping bacterioplanktonic communities among a set of >30 measured environmental parameters, and (iv) characterized how bacterioplankton structure varies according to the relative abundance of humic compounds, a by-product from the bacterial degradation process of allochthonous DOM.
Collapse
Affiliation(s)
| | - Sidki Bouslama
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
| | - Aleicia Holland
- La Trobe University, School of Life Science, Department of Ecology, Environment and Evolution, Centre for Freshwater Ecosystems, Albury/Wodonga Campus, Victoria, Australia
| | - Nicolas Leroux
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
| | - Pierre-Luc Mercier
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
| | - Adalberto Luis Val
- Instituto Nacional de Pesquisas da Amazônia, Laboratório de Ecofisiologia e Evolução Molecular, Manaus, Brazil
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
| |
Collapse
|
3
|
Gates K, Sandoval-Castillo J, Brauer CJ, Unmack PJ, Laporte M, Bernatchez L, Beheregaray LB. Environmental selection, rather than neutral processes, best explain regional patterns of diversity in a tropical rainforest fish. Heredity (Edinb) 2023:10.1038/s41437-023-00612-x. [PMID: 36997655 DOI: 10.1038/s41437-023-00612-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 03/14/2023] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
AbstractTo conserve the high functional and genetic variation in hotspots such as tropical rainforests, it is essential to understand the forces driving and maintaining biodiversity. We asked to what extent environmental gradients and terrain structure affect morphological and genomic variation across the wet tropical distribution of an Australian rainbowfish, Melanotaenia splendida splendida. We used an integrative riverscape genomics and morphometrics framework to assess the influence of these factors on both putative adaptive and non-adaptive spatial divergence. We found that neutral genetic population structure was largely explainable by restricted gene flow among drainages. However, environmental associations revealed that ecological variables had a similar power to explain overall genetic variation, and greater power to explain body shape variation, than the included neutral covariables. Hydrological and thermal variables were the strongest environmental predictors and were correlated with traits previously linked to heritable habitat-associated dimorphism in rainbowfishes. In addition, climate-associated genetic variation was significantly associated with morphology, supporting heritability of shape variation. These results support the inference of evolved functional differences among localities, and the importance of hydroclimate in early stages of diversification. We expect that substantial evolutionary responses will be required in tropical rainforest endemics to mitigate local fitness losses due to changing climates.
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Johnson O, Ribas CC, Aleixo A, Naka LN, Harvey MG, Brumfield RT. Amazonian birds in more dynamic habitats have less population genetic structure and higher gene flow. Mol Ecol 2023; 32:2186-2205. [PMID: 36798996 DOI: 10.1111/mec.16886] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023]
Abstract
Understanding the factors that govern variation in genetic structure across species is key to the study of speciation and population genetics. Genetic structure has been linked to several aspects of life history, such as foraging strategy, habitat association, migration distance, and dispersal ability, all of which might influence dispersal and gene flow. Comparative studies of population genetic data from species with differing life histories provide opportunities to tease apart the role of dispersal in shaping gene flow and population genetic structure. Here, we examine population genetic data from sets of bird species specialized on a series of Amazonian habitat types hypothesized to filter for species with dramatically different dispersal abilities: stable upland forest, dynamic floodplain forest, and highly dynamic riverine islands. Using genome-wide markers, we show that habitat type has a significant effect on population genetic structure, with species in upland forest, floodplain forest, and riverine islands exhibiting progressively lower levels of structure. Although morphological traits used as proxies for individual-level dispersal ability did not explain this pattern, population genetic measures of gene flow are elevated in species from more dynamic riverine habitats. Our results suggest that the habitat in which a species occurs drives the degree of population genetic structuring via its impact on long-term fluctuations in levels of gene flow, with species in highly dynamic habitats having particularly elevated gene flow. These differences in genetic variation across taxa specialized in distinct habitats may lead to disparate responses to environmental change or habitat-specific diversification dynamics over evolutionary time scales.
Collapse
Affiliation(s)
- Oscar Johnson
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Camila C Ribas
- Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brazil
| | - Alexandre Aleixo
- Museu Paraense Emílio Goeldi (MPEG), Belém, Pará, Brazil.,Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland.,Instituto Tecnológico Vale, Belém, Brazil
| | - Luciano N Naka
- Laboratório de Ecologia & Evolução de Aves, Departamento de Zoologia, Universidade Federal de Pernambuco, Recife, Brazil
| | - Michael G Harvey
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Robb T Brumfield
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, USA
| |
Collapse
|
6
|
Butler BO, Smith LL, Flores-Villela O. Phylogeography and taxonomy of Coleonyx elegans Gray 1845 (Squamata: Eublepharidae) in Mesoamerica: The Isthmus of Tehuantepec as an environmental barrier. Mol Phylogenet Evol 2023; 178:107632. [PMID: 36182052 DOI: 10.1016/j.ympev.2022.107632] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 08/05/2022] [Accepted: 09/23/2022] [Indexed: 12/14/2022]
Abstract
Population divergence leading to speciation is often explained by physical barriers causing allopatric distributions of historically connected populations. Environmental barriers have increasingly been shown to cause population divergence through local adaptation to distinct ecological characteristics. In this study, we evaluate population structuring and phylogeographic history within the Yucatán banded gecko Coleonyx elegans Gray 1845 to assess the role of both physical and environmental barriers in shaping the spatio-genetic distribution of a Mesoamerican tropical forest taxon. We generated RADseq and multi-locus Sanger datasets that included sampling across the entire species' range. Results find support for two distinct evolutionary lineages that diverged during the late Pliocene and show recent population expansions. Furthermore, these genetic lineages largely align with subspecies boundaries defined by morphology. Several mountain ranges identified as phylogeographic barriers in other taxa act as physical barriers to gene flow between the two clades. Despite the absence of a physical barrier between lineages across the lowland Isthmus of Tehuantepec, no introgression was observed. Here, a steep environmental cline associated with seasonality of precipitation corresponds exactly with the distributional limits of the lineages, whose closest samples are only 30 km apart. The combination of molecular and environmental evidence, and in conjunction with previous morphological evidence, allows us to reassess the current taxonomy in an integrative framework. Based on our findings, we elevate the previously recognized subspecies from the Pacific versant, the Colima banded gecko C. nemoralis Klauber 1945, to full species status and comment on conservation implications.
Collapse
Affiliation(s)
- Brett O Butler
- Museo de Zoología "Alfonso L. Herrera", Facultad de Ciencias, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, C. P. 04510 Coyoacán, CDMX, Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, C. P. 04510 Coyoacán, CDMX, Mexico.
| | - Lydia L Smith
- Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University of California, Berkeley, CA 94720, USA
| | - Oscar Flores-Villela
- Museo de Zoología "Alfonso L. Herrera", Facultad de Ciencias, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, C. P. 04510 Coyoacán, CDMX, Mexico
| |
Collapse
|
7
|
Anderson SAS, López-Fernández H, Weir JT. Ecology and the origin of non-ephemeral species. Am Nat 2022; 201:619-638. [PMID: 37130236 DOI: 10.1086/723763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AbstractResearch over the past three decades has shown that ecology-based extrinsic reproductive barriers can rapidly arise to generate incipient species-but such barriers can also rapidly dissolve when environments change, resulting in incipient species collapse. Understanding the evolution of unconditional, "intrinsic" reproductive barriers is therefore important for understanding the longer-term buildup of biodiversity. In this article, we consider ecology's role in the evolution of intrinsic reproductive isolation. We suggest that this topic has fallen into a gap between disciplines: while evolutionary ecologists have traditionally focused on the rapid evolution of extrinsic isolation between co-occurring ecotypes, speciation geneticists studying intrinsic isolation in other taxa have devoted little attention to the ecological context in which it evolves. We argue that for evolutionary ecology to close this gap, the field will have to expand its focus beyond rapid adaptation and its traditional model systems. Synthesizing data from several subfields, we present circumstantial evidence for and against different forms of ecological adaptation as promoters of intrinsic isolation and discuss alternative forces that may be significant. We conclude by outlining complementary approaches that can better address the role of ecology in the evolution of nonephemeral reproductive barriers and, by extension, less ephemeral species.
Collapse
|
8
|
dos Santos MV, Prudente ALC, Rodrigues MT, Sturaro MJ. The Role of Vicariance and Paleoclimatic Shifts in the Diversification of Uranoscodon superciliosus (Squamata, Tropiduridae) of the Amazonian Floodplains. Evol Biol 2022. [DOI: 10.1007/s11692-022-09583-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
9
|
Sylvain FÉ, Normandeau E, Holland A, Luis Val A, Derome N. Genomics of Serrasalmidae teleosts through the lens of microbiome fingerprinting. Mol Ecol 2022; 31:4656-4671. [PMID: 35729748 DOI: 10.1111/mec.16574] [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: 09/02/2021] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 11/28/2022]
Abstract
Associations between host genotype and host-associated microbiomes have been shown in a variety of animal clades, but studies on teleosts mostly show weak associations. Our study aimed to explore these relationships in four sympatric Serrasalmidae (i.e. piranha) teleosts from an Amazonian lake, using datasets from the hosts genomes (SNPs from GBS), skin and gut microbiomes (16S rRNA gene metataxonomics), and diets (COI metabarcoding) from the same fish individuals. Firstly, we investigated whether there were significant covariations of microbiome and fish genotypes at the inter and intraspecific levels. We also assessed the extent of co-variation between Serrasalmidae diet and microbiome, to isolate genotypic from dietary effects on community structure. We observed a significant covariation of skin microbiomes and host genotypes at interspecific (R2 =24.4%) and intraspecific (R2 =6.2%) levels, whereas gut microbiomes correlated poorly with host genotypes. Serrasalmidae diet composition was significantly correlated to fish genotype only at the interspecific level (R2 =5.4%), but did not covary with gut microbiome composition (mantel R=-0.04). Secondly, we investigated whether the study of interspecific differentiation could benefit from considering host associated microbial communities in addition to host genotypes. By using a NMDS ordination-based approach, we observed that ordinations from skin and gut species-specific bacterial biomarkers identified through a random forest algorithm, could significantly increase the average interspecific differentiation detected through host genotype data alone. Although future studies encompassing additional species and environments are needed, our results suggest Serrasalmidae microbiomes could constitute an insightful trait to be considered when studying the interspecific differences between members of this clade.
Collapse
Affiliation(s)
- François-Étienne Sylvain
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 avenue de la Médecine, Québec (QC), G1V 0A6, Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 avenue de la Médecine, Québec (QC), G1V 0A6, Canada
| | - Aleicia Holland
- La Trobe University, School of Life Science, Department of Ecology, Environment and Evolution, Albury/Wodonga Campus, Vic, Australia
| | - Adalberto Luis Val
- Instituto Nacional de Pesquisas da Amazônia (INPA), Laboratório de Ecofisiologia e Evolução Molecular, Manaus, AM, 69067-375, Brazil
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 avenue de la Médecine, Québec (QC), G1V 0A6, Canada
| |
Collapse
|
10
|
Leroux N, Sylvain FÉ, Normandeau E, Holland A, Val AL, Derome N. Evolution of an Amazonian Fish Is Driven by Allopatric Divergence Rather Than Ecological Divergence. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.875961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Lowland central Amazonia is characterized by heterogeneous riverscapes dominated by two chemically divergent water types: black (ion-poor, rich in dissolved organic carbonate and acidic) and white (rich in nutrient and turbid) waters. Recent phylogeographic and genomic studies have associated the ecotone formed by these environments to an ecologically driven genetic divergence between fish present in both water types. With the objective of better understanding the evolutionary forces behind the central Amazonian teleostean diversification, we sampled 240 Mesonauta festivus from 12 sites on a wide area of the Amazonian basin. These sites included three confluences of black and white water environments to seek for repeated evidences of ecological divergence at the junction of these ecotones. Results obtained through our genetic assessment based on 41,268 single nucleotide polymorphism (SNPs) contrast with previous findings and support a low influence of diverging water physicochemical characteristics on the genetic structuration of M. festivus populations. Conversely, we detected patterns of isolation by downstream water current and evidence of past events of vicariance potentially linked to the Amazon River formation. Using a combination of population genetics, phylogeographic analysis and environmental association models, we decomposed the spatial and environmental genetic variances to assess which evolutionary forces shaped inter-population differences in M. festivus’ genome. Our sampling design, comprising three confluences of black and white water rivers, supports the main role of evolution by allopatry. While an ecologically driven evolution admittedly played a role in Amazonian fish diversification, we argue that neutral evolutionary processes explain most of the divergence between M. festivus populations.
Collapse
|
11
|
Phylogeographic structure suggests environmental gradient speciation in a montane frog from the northern Andes of Colombia. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00549-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
12
|
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.
Collapse
|
13
|
Hay AC, Sandoval-Castillo J, Cooke GM, Chao NL, Beheregaray LB. Riverscape Genomics Clarifies Neutral and Adaptive Evolution in an Amazonian Characin Fish (Triportheus albus). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.825406] [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
Understanding the role of natural selection in the evolution of wild populations is challenging due to the spatial complexity of natural systems. The richest diversity of freshwater fishes in the world is found in the Amazon Basin, a system where marked hydrochemical differences exist at the interface of major rivers with distinct “water colors” (i.e., black, white, and clear water). We hypothesize that divergent natural selection associated with these “aquatic ecotones” influences population-level adaptive divergence in the non-migratory Amazonian fish fauna. This hypothesis was tested using a landscape genomics framework to compare the relative contribution of environmental and spatial factors to the evolutionary divergence of the Amazonian characin fish Triportheus albus. The framework was based on spatial data, in situ hydrochemical measurements, and 15,251 filtered SNPs (single nucleotide polymorphisms) for T. albus sampled from three major Amazonian rivers. Gradient Forest, redundancy analysis (RDA) and BayPass analyses were used to test for signals of natural selection, and model-based and model-free approaches were used to evaluate neutral population differentiation. After controlling for a signal of neutral hierarchical structure which was consistent with the expectations for a dendritic system, variation in turbidity and pH were key factors contributing to adaptive divergence. Variation in genes involved in acid-sensitive ion transport pathways and light-sensitive photoreceptor pathways was strongly associated with pH and turbidity variability. This study improves our understanding of how natural selection and neutral evolution impact on the distribution of aquatic biodiversity from the understudied and ecologically complex Amazonia.
Collapse
|
14
|
Fouquet A, Cornuault J, Rodrigues MT, Werneck FP, Hrbek T, Acosta-Galvis AR, Massemin D, J. R. Kok P, Ernst R. Diversity, biogeography and reproductive evolution in the genus Pipa (Amphibia: Anura: Pipidae). Mol Phylogenet Evol 2022; 170:107442. [DOI: 10.1016/j.ympev.2022.107442] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/22/2021] [Accepted: 02/16/2022] [Indexed: 11/29/2022]
|
15
|
Thomé MTC, Carstens BC, Rodrigues MT, Galetti PM, Alexandrino J, Haddad CFB. A role of asynchrony of seasons in explaining genetic differentiation in a Neotropical toad. Heredity (Edinb) 2021; 127:363-372. [PMID: 34304245 PMCID: PMC8478927 DOI: 10.1038/s41437-021-00460-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 07/09/2021] [Accepted: 07/11/2021] [Indexed: 02/07/2023] Open
Abstract
The process of diversification can be studied at the phylogeographic level by attempting to identify the environmental features that promote and maintain population divergence. Here we investigate diversification in Rhinella granulosa, a Neotropical toad from northeastern Brazil, by testing a range of hypotheses that encompass different putative mechanisms reducing gene flow among populations. We sequenced single nucleotide polymorphisms and examined individual predictions related to the role of geographic barriers (rivers), ecological gradients, historical habitat stability, and spatial variation in climate seasonality, also known as the asynchrony of seasons hypothesis. This hypothesis postulates that temporal asynchrony of wet and dry seasons over short distances causes parapatric populations to become isolated by time. After determining genetic structure, inferring past distributions, ranking demographic models, and estimating the power of monthly climatic variables, our results identified two populations that are not associated with geographic barriers, biome gradients, or historical refugia. Instead, they are predicted by spatial variation in monthly rainfall and minimum temperature, consistent with the asynchrony of seasons hypothesis, supported also by our comparative framework using multiple matrix regression and linear mixed effects modeling. Due to the toad's life history, climate likely mediates gene flow directly, with genetic differentiation being provoked by neutral mechanisms related to climate driven population isolation, and/or by natural selection against migrants from populations with different breeding times. The asynchrony of seasons hypothesis is seldom considered in phylogeographic studies, but our results indicate that it should be tested in systems where breeding is tightly coupled with climate.
Collapse
Affiliation(s)
- Maria Tereza C Thomé
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA.
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil.
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Miguel Trefaut Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Pedro Manoel Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - João Alexandrino
- Departamento de Ecologia e Biologia Evolutiva, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, SP, Brazil
| | - Célio F B Haddad
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil
| |
Collapse
|
16
|
Silva SM, Ribas CC, Aleixo A. Recent population differentiation in the habitat specialist Glossy Antshrike (Aves: Thamnophilidae) across Amazonian seasonally flooded forests. Ecol Evol 2021; 11:11826-11838. [PMID: 34522344 PMCID: PMC8427616 DOI: 10.1002/ece3.7951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 07/11/2021] [Accepted: 07/13/2021] [Indexed: 11/30/2022] Open
Abstract
We assessed population structure and the spatio-temporal pattern of diversification in the Glossy Antshrike Sakesphorus luctuosus (Aves, Thamnophilidae) to understand the processes shaping the evolutionary history of Amazonian floodplains and address unresolved taxonomic controversies surrounding its species limits. By targeting ultraconserved elements (UCEs) from 32 specimens of S. luctuosus, we identified independent lineages and estimated their differentiation, divergence times, and migration rates. We also estimated current and past demographic histories for each recovered lineage. We found evidence confirming that S. luctuosus consists of a single species, comprising at least four populations, with some highly admixed individuals and overall similar levels of migration between populations. We confirmed the differentiation of the Araguaia River basin population (S. l. araguayae) and gathered circumstantial evidence indicating that the taxon S. hagmanni may represent a highly introgressed population between three distinct phylogroups of S. luctuosus. Divergences between populations occurred during the last 1.2 mya. Signs of population expansions were detected for populations attributed to subspecies S. l. luctuosus, but not for the S. l. araguayae population. Our results support that S. luctuosus has had a complex population history, resulting from a high dependence on southeastern "clear water" seasonally flooded habitats and their availability through time. Spatial and demographic expansions toward the western "white water" flooded forests might be related to recent changes in connectivity and availability of these habitats. Our study reinforces the view that isolation due to absence of suitable habitat has been an important driver of population differentiation within Amazonian flooded forests, but also that differences between várzeas ("white water" floodplains, mostly in southwestern Amazonia) and igapós ("clear water" floodplains, especially located in the east) should be further explored as drivers of micro-evolution for terrestrial species.
Collapse
Affiliation(s)
- Sofia Marques Silva
- Research Centre in Biodiversity and Genetic ResourcesCIBIO/InBIOVairãoPortugal
- Department of ZoologyMuseu Paraense Emílio GoeldiBelémBrazil
| | | | - Alexandre Aleixo
- Department of ZoologyMuseu Paraense Emílio GoeldiBelémBrazil
- Finnish Museum of Natural HistoryUniversity of HelsinkiHelsinkiFinland
| |
Collapse
|
17
|
Couvreur TL, Dauby G, Blach‐Overgaard A, Deblauwe V, Dessein S, Droissart V, Hardy OJ, Harris DJ, Janssens SB, Ley AC, Mackinder BA, Sonké B, Sosef MS, Stévart T, Svenning J, Wieringa JJ, Faye A, Missoup AD, Tolley KA, Nicolas V, Ntie S, Fluteau F, Robin C, Guillocheau F, Barboni D, Sepulchre P. Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna. Biol Rev Camb Philos Soc 2021; 96:16-51. [PMID: 32924323 PMCID: PMC7821006 DOI: 10.1111/brv.12644] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 12/30/2022]
Abstract
Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.
Collapse
Affiliation(s)
| | - Gilles Dauby
- AMAP Lab, IRD, CIRAD, CNRS, INRAUniversity of MontpellierMontpellierFrance
- Laboratoire d'évolution Biologique et Ecologie, Faculté des SciencesUniversité Libre de BruxellesCP160/12, Avenue F.D. Roosevelt 50Brussels1050Belgium
| | - Anne Blach‐Overgaard
- Section for Ecoinformatics & Biodiversity, Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
| | - Vincent Deblauwe
- Center for Tropical Research (CTR), Institute of the Environment and SustainabilityUniversity of California, Los Angeles (UCLA)Los AngelesCA90095U.S.A.
- International Institute of Tropical Agriculture (IITA)YaoundéCameroon
| | | | - Vincent Droissart
- AMAP Lab, IRD, CIRAD, CNRS, INRAUniversity of MontpellierMontpellierFrance
- Laboratoire de Botanique Systématique et d'Écologie, École Normale SupérieureUniversité de Yaoundé IPO Box 047YaoundéCameroon
- Herbarium et Bibliothèque de Botanique AfricaineUniversité Libre de BruxellesBoulevard du TriompheBrusselsB‐1050Belgium
- Africa & Madagascar DepartmentMissouri Botanical GardenSt. LouisMOU.S.A.
| | - Oliver J. Hardy
- Laboratoire d'évolution Biologique et Ecologie, Faculté des SciencesUniversité Libre de BruxellesCP160/12, Avenue F.D. Roosevelt 50Brussels1050Belgium
| | - David J. Harris
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghU.K.
| | | | - Alexandra C. Ley
- Institut für Geobotanik und Botanischer GartenUniversity Halle‐WittenbergNeuwerk 21Halle06108Germany
| | | | - Bonaventure Sonké
- Laboratoire de Botanique Systématique et d'Écologie, École Normale SupérieureUniversité de Yaoundé IPO Box 047YaoundéCameroon
| | | | - Tariq Stévart
- Herbarium et Bibliothèque de Botanique AfricaineUniversité Libre de BruxellesBoulevard du TriompheBrusselsB‐1050Belgium
- Africa & Madagascar DepartmentMissouri Botanical GardenSt. LouisMOU.S.A.
| | - Jens‐Christian Svenning
- Section for Ecoinformatics & Biodiversity, Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
| | - Jan J. Wieringa
- Naturalis Biodiversity CenterDarwinweg 2Leiden2333 CRThe Netherlands
| | - Adama Faye
- Laboratoire National de Recherches sur les Productions Végétales (LNRPV)Institut Sénégalais de Recherches Agricoles (ISRA)Route des Hydrocarbures, Bel Air BP 1386‐ CP18524DakarSenegal
| | - Alain D. Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of ScienceUniversity of DoualaPO Box 24157DoualaCameroon
| | - Krystal A. Tolley
- South African National Biodiversity InstituteKirstenbosch Research CentrePrivate Bag X7, ClaremontCape Town7735South Africa
- School of Animal, Plant and Environmental SciencesUniversity of the WitwatersrandPrivate Bag 3Wits2050South Africa
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHEUniversité des AntillesCP51, 57 rue CuvierParis75005France
| | - Stéphan Ntie
- Département de Biologie, Faculté des SciencesUniversité des Sciences et Techniques de MasukuFrancevilleBP 941Gabon
| | - Frédiéric Fluteau
- Institut de Physique du Globe de Paris, CNRSUniversité de ParisParisF‐75005France
| | - Cécile Robin
- CNRS, Géosciences Rennes, UMR6118University of RennesRennes35042France
| | | | - Doris Barboni
- CEREGE, Aix‐Marseille University, CNRS, IRD, Collège de France, INRA, Technopole Arbois MéditerranéeBP80Aix‐en‐Provence cedex413545France
| | - Pierre Sepulchre
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA‐CNRS‐UVSQUniversité Paris‐SaclayGif‐sur‐YvetteF‐91191France
| |
Collapse
|
18
|
Da Silva MF, Cruz MV, Vidal Júnior JDD, Zucchi MI, Mori GM, De Souza AP. Geographical and environmental contributions to genomic divergence in mangrove forests. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Assessing the relative importance of geographical and environmental factors to the spatial distribution of genetic variation can provide information about the processes that maintain genetic variation in natural populations. With a globally wide but very restricted habitat distribution, mangrove trees are a useful model for studies aiming to understand the contributions of these factors. Mangroves occur along the continent–ocean interface of tropical and subtropical latitudes, regions considered inhospitable to many other types of plants. Here, we used landscape genomics approaches to investigate the relative contributions of geographical and environmental variables to the genetic variation of two black mangrove species, Avicennia schaueriana and Avicennia germinans, along the South American coast. Using single nucleotide polymorphisms, our results revealed an important role of ocean currents and geographical distance in the gene flow of A. schaueriana and an isolation-by-environment pattern in the organization of the genetic diversity of A. germinans. Additionally, for A. germinans, we observed significant correlations between genetic variation with evidence of selection and the influence of precipitation regimens, solar radiation and temperature patterns. These discoveries expand our knowledge about the evolution of mangrove trees and provide important information to predict future responses of coastal species to the expected global changes during this century.
Collapse
Affiliation(s)
- Michele Fernandes Da Silva
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Mariana Vargas Cruz
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - João De Deus Vidal Júnior
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Gustavo Maruyama Mori
- Institute of Biosciences, São Paulo State University (UNESP), São Vicente, SP, Brazil
| | - Anete Pereira De Souza
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| |
Collapse
|
19
|
Borghezan EDA, Pires THDS, Ikeda T, Zuanon J, Kohshima S. A Review on Fish Sensory Systems and Amazon Water Types With Implications to Biodiversity. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.589760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The Amazon has the highest richness of freshwater organisms in the world, which has led to a multitude of hypotheses on the mechanisms that generated this biodiversity. However, most of these hypotheses focus on the spatial distance of populations, a framework that fails to provide an explicit mechanism of speciation. Ecological conditions in Amazon freshwaters can be strikingly distinct, as it has been recognized since Alfred Russel Wallace’s categorization into black, white, and blue (= clear) waters. Water types reflect differences in turbidity, dissolved organic matter, electrical conductivity, pH, amount of nutrients and lighting environment, characteristics that directly affect the sensory abilities of aquatic organisms. Since natural selection drives evolution of sensory systems to function optimally according to environmental conditions, the sensory systems of Amazon freshwater organisms are expected to vary according to their environment. When differences in sensory systems affect chances of interbreeding between populations, local adaptations may result in speciation. Here, we briefly present the limnologic characteristics of Amazonian water types and how they are expected to influence photo-, chemical-, mechano-, and electro-reception of aquatic organisms, focusing on fish. We put forward that the effect of different water types on the adaptation of sensory systems is an important mechanism that contributed to the evolution of fish diversity. We point toward underexplored research perspectives on how divergent selection may act on sensory systems and thus contribute to the origin and maintenance of the biodiversity of Amazon aquatic environments.
Collapse
|
20
|
Leal BSS, Brandão MM, Palma-Silva C, Pinheiro F. Differential gene expression reveals mechanisms related to habitat divergence between hybridizing orchids from the Neotropical coastal plains. BMC PLANT BIOLOGY 2020; 20:554. [PMID: 33302865 PMCID: PMC7731501 DOI: 10.1186/s12870-020-02757-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/25/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Closely related hybridizing species are ideal systems for identifying genomic regions underlying adaptive divergence. Although gene expression plays a central role in determining ecologically-based phenotypic differences, few studies have inferred the role of gene expression for adaptive divergence in Neotropical systems. In this study, we conduct genome-wide expression analysis alongside soil elemental analysis in sympatric and allopatric populations of Epidendrum fulgens and E. puniceoluteum (Orchidaceae), which occur in contrasting adjacent habitats in the Neotropical coastal plains. RESULTS These species were highly differentiated by their gene expression profiles, as determined by 18-21% of transcripts. Gene ontology (GO) terms associated with reproductive processes were enriched according to comparisons between species in both allopatric and sympatric populations. Species showed differential expression in genes linked to salt and waterlogging tolerance according to comparisons between species in sympatry, and biological processes related to environmental stimulus appeared as representative among those transcripts associated with edaphic characteristics in each sympatric zone. Hybrids, in their turn, were well differentiated from E. fulgens, but exhibited a similar gene expression profile to flooding-tolerant E. puniceolutem. When compared with parental species, hybrids showed no transcripts with additive pattern of expression and increased expression for almost all transgressive transcripts. CONCLUSIONS This study sheds light on general mechanisms promoting ecological differentiation and assortative mating, and suggests candidate genes, such as those encoding catalase and calcium-dependent protein kinase, underling adaptation to harsh edaphic conditions in the Neotropical coastal plains. Moreover, it demonstrates that differential gene expression plays a central role in determining ecologically-based phenotypic differences among co-occurring species and their hybrids.
Collapse
Affiliation(s)
| | - Marcelo Mendes Brandão
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, 13083-862, Brazil
| | - Clarisse Palma-Silva
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Campinas, SP, 13083-862, Brazil
| | - Fabio Pinheiro
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Campinas, SP, 13083-862, Brazil
| |
Collapse
|
21
|
Landscape and Climate Influence the Patterns of Genetic Diversity and Inbreeding in Cerrado Plant Species. DIVERSITY 2020. [DOI: 10.3390/d12110421] [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
The anthropization of the landscape of the Cerrado biome that has occurred over the past few decades has fragmented its natural environments, impacting the connectivity of the plant populations and altering their gene flow. Plant species may also reduce population size in response to sub-optimal climatic and environmental conditions, and observed distribution patterns may align with theoretical schemes, such as the center–periphery model, that is, it is possible that populations on the edge have lower genetic diversity than center populations, theoretically submitted to environmental conditions closer to the optimum. In this context, we evaluate whether the genetic diversity and inbreeding coefficients of Cerrado plant species are affected by landscape features and climate characteristics, and in particular, if the distribution of the genetic diversity of these plants is consistent with the center–periphery model. To do this, we conducted a literature search for genetic studies of Cerrado plant populations using Scopus, Web of Science, and Scielo databases and the species found were used as a proxy to explore patterns throughout the biome. The data were analyzed using generalized linear mixed models (GLMM) and multiple matrix regressions (MMRRs) to evaluate the effects of landscape features and climatic variables on the observed (HO) and expected heterozygosity (HE), allelic richness (AR) and inbreeding (Fis) patterns of the local populations. The landscape was evaluated in terms of the percentage land cover of agriculture (AG), forestry (FO), remnant vegetation (RV), urban areas (UA), pasture (PA), and water (WA) within buffers of 1 km, 3 km, and 5 km around the study populations. We analyzed 121 populations of 31 plant species. The GLMMs showed that HO was affected by FO regardless of buffer size, while HE was also affected by FO, but also by WA and UA. AR was affected by WA and UA in all three buffer zones while the Fis was affected by FO and AU. The MMRRs showed that WA may affect HO, HE, and Fis within the 1 km buffer, while FO affects HO and UA affects AR within the 5 km buffer. In the case of the 1 km and 3 km buffers, however, the geographic distance between populations was identified as a factor determining the genetic diversity and inbreeding indices, indicating that isolation by distance may be an important factor defining the breeding patterns of the Cerrado plant populations. The GLMMs and MMRRs also showed that the mean annual temperature (MAT) and, to a lesser extent, isothermality (ISO) can explain the variation in genetic diversity observed in the Cerrado plant populations. We also found that the center–periphery model fits the distribution pattern observed in most of the species evaluated, including Annona crassiflora,Annona coriacea, Copaifera langsdorffii, and Eugenia dysenterica. Our results indicate that changes in the climate and the landscape of Brazilian Cerrado must be considered carefully to guarantee minimizing the impacts of these processes on the genetic diversity of Cerrado plant species and ensuring the long-term conservation of these species in this biome.
Collapse
|
22
|
Albert JS, Tagliacollo VA, Dagosta F. Diversification of Neotropical Freshwater Fishes. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011620-031032] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Neotropical freshwater fishes (NFFs) constitute the most diverse continental vertebrate fauna on Earth, with more than 6,200 named species compressed into an aquatic footprint <0.5% of the total regional land-surface area and representing the greatest phenotypic disparity and functional diversity of any continental ichthyofauna. Data from the fossil record and time-calibrated molecular phylogenies indicate that most higher taxa (e.g., genera, families) diversified relatively continuously through the Cenozoic, across broad geographic ranges of the South American platform. Biodiversity data for most NFF clades support a model of continental radiation rather than adaptive radiation, in which speciation occurs mainly in allopatry, and speciation and adaptation are largely decoupled. These radiations occurred under the perennial influence of river capture and sea-level oscillations, which episodically fragmented and merged portions of adjacent river networks. The future of the NFF fauna into the Anthropocene is uncertain, facing numerous threats at local, regional, and continental scales.
Collapse
Affiliation(s)
- James S. Albert
- Department of Biology, University of Louisiana at Lafayette, Louisiana 70504, USA
| | | | - Fernando Dagosta
- Faculty of Biological and Environmental Sciences, Universidade Federal da Grande Dourados, Brazil 79825-070
| |
Collapse
|
23
|
Linck E, Freeman BG, Dumbacher JP. Speciation and gene flow across an elevational gradient in New Guinea kingfishers. J Evol Biol 2020; 33:1643-1652. [PMID: 32916016 DOI: 10.1111/jeb.13698] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/24/2020] [Accepted: 08/29/2020] [Indexed: 01/01/2023]
Abstract
Closely related species with parapatric elevational ranges are ubiquitous in tropical mountains worldwide. The gradient speciation hypothesis proposes that these series are the result of in situ ecological speciation driven by divergent selection across elevation. Direct tests of this scenario have been hampered by the difficulty inferring the geographic arrangement of populations at the time of divergence. In cichlids, sticklebacks and Timema stick insects, support for ecological speciation driven by other selective pressures has come from demonstrating parallel speciation, where divergence proceeds independently across replicated environmental gradients. Here, we take advantage of the unique geography of the island of New Guinea to test for parallel gradient speciation in replicated populations of Syma kingfishers that show extremely subtle differentiation across elevation and between historically isolated mountain ranges. We find that currently described high-elevation and low-elevation species have reciprocally monophyletic gene trees and form nuclear DNA clusters, rejecting this hypothesis. However, demographic modelling suggests selection has likely maintained species boundaries in the face of gene flow following secondary contact. We compile evidence from the published literature to show that although in situ gradient speciation in labile organisms such as birds appears rare, divergent selection and post-speciation gene flow may be an underappreciated force in the origin of elevational series and tropical beta diversity along mountain slopes.
Collapse
Affiliation(s)
- Ethan Linck
- Department of Biology & Burke Museum of Natural History & Culture, University of Washington, Seattle, WA, USA
| | - Benjamin G Freeman
- Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - John P Dumbacher
- Ornithology & Mammalogy, California Academy of Sciences, San Francisco, CA, USA
| |
Collapse
|
24
|
Ferreira AS, Lima AP, Jehle R, Ferrão M, Stow A. The Influence of Environmental Variation on the Genetic Structure of a Poison Frog Distributed Across Continuous Amazonian Rainforest. J Hered 2020; 111:457-470. [PMID: 32827440 DOI: 10.1093/jhered/esaa034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 08/20/2020] [Indexed: 11/13/2022] Open
Abstract
Biogeographic barriers such as rivers have been shown to shape spatial patterns of biodiversity in the Amazon basin, yet relatively little is known about the distribution of genetic variation across continuous rainforest. Here, we characterize the genetic structure of the brilliant-thighed poison frog (Allobates femoralis) across an 880-km-long transect along the Purus-Madeira interfluve south of the Amazon river, based on 64 individuals genotyped at 7609 single-nucleotide polymorphism (SNP) loci. A population tree and clustering analyses revealed 4 distinct genetic groups, one of which was strongly divergent. These genetic groups were concomitant with femoral spot coloration differences, which was intermediate within a zone of admixture between two of the groups. The location of these genetic groups did not consistently correspond to current ecological transitions between major forest types. A multimodel approach to quantify the relative influence of isolation-by-geographic distance (IBD) and isolation-by-environmental resistance (IBR) nevertheless revealed that, in addition to a strong signal of IBD, spatial genetic differentiation was explained by IBR primarily linked to dry season intensity (r2 = 8.4%) and canopy cover (r2 = 6.4%). We show significant phylogenetic divergence in the absence of obvious biogeographical barriers and that finer-scaled measures of genetic structure are associated with environmental variables also known to predict the density of A. femoralis.
Collapse
Affiliation(s)
- Anthony S Ferreira
- Programa de Capacitação Institucional, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Albertina P Lima
- Coordenacão de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Robert Jehle
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Miquéias Ferrão
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Adam Stow
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| |
Collapse
|
25
|
Blanchet S, Prunier JG, Paz‐Vinas I, Saint‐Pé K, Rey O, Raffard A, Mathieu‐Bégné E, Loot G, Fourtune L, Dubut V. A river runs through it: The causes, consequences, and management of intraspecific diversity in river networks. Evol Appl 2020; 13:1195-1213. [PMID: 32684955 PMCID: PMC7359825 DOI: 10.1111/eva.12941] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/14/2020] [Accepted: 02/19/2020] [Indexed: 01/01/2023] Open
Abstract
Rivers are fascinating ecosystems in which the eco-evolutionary dynamics of organisms are constrained by particular features, and biologists have developed a wealth of knowledge about freshwater biodiversity patterns. Over the last 10 years, our group used a holistic approach to contribute to this knowledge by focusing on the causes and consequences of intraspecific diversity in rivers. We conducted empirical works on temperate permanent rivers from southern France, and we broadened the scope of our findings using experiments, meta-analyses, and simulations. We demonstrated that intraspecific (genetic) diversity follows a spatial pattern (downstream increase in diversity) that is repeatable across taxa (from plants to vertebrates) and river systems. This pattern can result from interactive processes that we teased apart using appropriate simulation approaches. We further experimentally showed that intraspecific diversity matters for the functioning of river ecosystems. It indeed affects not only community dynamics, but also key ecosystem functions such as litter degradation. This means that losing intraspecific diversity in rivers can yield major ecological effects. Our work on the impact of multiple human stressors on intraspecific diversity revealed that-in the studied river systems-stocking of domestic (fish) strains strongly and consistently alters natural spatial patterns of diversity. It also highlighted the need for specific analytical tools to tease apart spurious from actual relationships in the wild. Finally, we developed original conservation strategies at the basin scale based on the systematic conservation planning framework that appeared pertinent for preserving intraspecific diversity in rivers. We identified several important research avenues that should further facilitate our understanding of patterns of local adaptation in rivers, the identification of processes sustaining intraspecific biodiversity-ecosystem function relationships, and the setting of reliable conservation plans.
Collapse
Affiliation(s)
- Simon Blanchet
- Centre National pour la Recherche ScientifiqueStation d'Écologie Théorique et Expérimentale du CNRS à MoulisUniversité Toulouse III Paul SabatierUMR‐5321MoulisFrance
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
| | - Jérôme G. Prunier
- Centre National pour la Recherche ScientifiqueStation d'Écologie Théorique et Expérimentale du CNRS à MoulisUniversité Toulouse III Paul SabatierUMR‐5321MoulisFrance
| | - Ivan Paz‐Vinas
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
- Laboratoire Ecologie Fonctionnelle et EnvironnementUniversité de ToulouseUPSCNRSINPUMR‐5245 ECOLABToulouseFrance
| | - Keoni Saint‐Pé
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
| | - Olivier Rey
- IHPEUniv. MontpellierCNRSIfremerUniv. Perpignan Via DomitiaPerpignanFrance
| | - Allan Raffard
- Centre National pour la Recherche ScientifiqueStation d'Écologie Théorique et Expérimentale du CNRS à MoulisUniversité Toulouse III Paul SabatierUMR‐5321MoulisFrance
| | - Eglantine Mathieu‐Bégné
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
- IHPEUniv. MontpellierCNRSIfremerUniv. Perpignan Via DomitiaPerpignanFrance
| | - Géraldine Loot
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
| | - Lisa Fourtune
- Centre National pour la Recherche ScientifiqueLaboratoire Evolution & Diversité BiologiqueInstitut de Recherche pour le DéveloppementUniversité Toulouse III Paul SabatierUMR‐5174 EDBToulouseFrance
- PEIRENEEA 7500Université de LimogesLimogesFrance
| | - Vincent Dubut
- Aix Marseille UniversitéCNRSIRDAvignon UniversitéIMBEMarseilleFrance
| |
Collapse
|
26
|
|
27
|
Moreno-Contreras I, Sánchez-González LA, Arizmendi MDC, Prieto-Torres DA, Navarro-Sigüenza AG. Climatic Niche Evolution in the Arremon brunneinucha Complex (Aves: Passerellidae) in a Mesoamerican Landscape. Evol Biol 2020. [DOI: 10.1007/s11692-020-09498-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
28
|
Thom G, Xue AT, Sawakuchi AO, Ribas CC, Hickerson MJ, Aleixo A, Miyaki C. Quaternary climate changes as speciation drivers in the Amazon floodplains. SCIENCE ADVANCES 2020; 6:eaax4718. [PMID: 32195336 PMCID: PMC7065905 DOI: 10.1126/sciadv.aax4718] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 12/13/2019] [Indexed: 05/04/2023]
Abstract
The role of climate as a speciation driver in the Amazon has long been discussed. Phylogeographic studies have failed to recover synchronous demographic responses across taxa, although recent evidence supports the interaction between rivers and climate in promoting speciation. Most studies, however, are biased toward upland forest organisms, while other habitats are poorly explored and could hold valuable information about major historical processes. We conducted a comparative phylogenomic analysis of floodplain forest birds to explore the effects of historical environmental changes and current connectivity on population differentiation. Our findings support a similar demographic history among species complexes, indicating that the central portion of the Amazon River basin is a suture zone for taxa isolated across the main Amazonian sub-basins. Our results also suggest that changes in the fluvial landscape induced by climate variation during the Mid- and Late Pleistocene drove population isolation, leading to diversification with subsequent secondary contact.
Collapse
Affiliation(s)
- Gregory Thom
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP 05508-090, Brazil
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA
| | - Alexander T Xue
- Department of Biology, Marshak Science Building, City College of New York, New York, NY 10031, USA
- Human Genetics Institute of New Jersey and Department of Genetics, Rutgers University, 604 Allison Road, Piscataway, NJ 08854, USA
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - André O Sawakuchi
- Instituto de Geociências, Universidade de São Paulo, Rua do Lago 562, São Paulo, SP 05508-080, Brazil
| | - Camila C Ribas
- Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo 2936, Manaus, AM 69060-001, Brazil
| | - Michael J Hickerson
- Department of Biology, Marshak Science Building, City College of New York, New York, NY 10031, USA
- The Graduate Center, City University of New York, New York, NY 10016, USA
- New York Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Alexandre Aleixo
- Museu Paraense Emílio Goeldi (MPEG), Caixa Postal 399, Belém, PA 66040-170, Brazil
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Cristina Miyaki
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP 05508-090, Brazil
| |
Collapse
|
29
|
Oberdorff T, Dias MS, Jézéquel C, Albert JS, Arantes CC, Bigorne R, Carvajal-Valleros FM, De Wever A, Frederico RG, Hidalgo M, Hugueny B, Leprieur F, Maldonado M, Maldonado-Ocampo J, Martens K, Ortega H, Sarmiento J, Tedesco PA, Torrente-Vilara G, Winemiller KO, Zuanon J. Unexpected fish diversity gradients in the Amazon basin. SCIENCE ADVANCES 2019; 5:eaav8681. [PMID: 31535018 PMCID: PMC6739107 DOI: 10.1126/sciadv.aav8681] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 08/08/2019] [Indexed: 05/31/2023]
Abstract
Using the most comprehensive fish occurrence database, we evaluated the importance of ecological and historical drivers in diversity patterns of subdrainage basins across the Amazon system. Linear models reveal the influence of climatic conditions, habitat size and sub-basin isolation on species diversity. Unexpectedly, the species richness model also highlighted a negative upriver-downriver gradient, contrary to predictions of increasing richness at more downriver locations along fluvial gradients. This reverse gradient may be linked to the history of the Amazon drainage network, which, after isolation as western and eastern basins throughout the Miocene, only began flowing eastward 1-9 million years (Ma) ago. Our results suggest that the main center of fish diversity was located westward, with fish dispersal progressing eastward after the basins were united and the Amazon River assumed its modern course toward the Atlantic. This dispersal process seems not yet achieved, suggesting a recent formation of the current Amazon system.
Collapse
Affiliation(s)
- Thierry Oberdorff
- UMR EDB (Laboratoire Évolution et Diversité Biologique), CNRS 5174, IRD253, UPS; 118 route de Narbonne, F-31062 Toulouse, France
| | - Murilo S. Dias
- Departamento de Ecologia, Universidade de Brasília, Brasilia, DF, Brazil
| | - Céline Jézéquel
- UMR EDB (Laboratoire Évolution et Diversité Biologique), CNRS 5174, IRD253, UPS; 118 route de Narbonne, F-31062 Toulouse, France
| | - James S. Albert
- University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Caroline C. Arantes
- Center for Global Change and Earth Observations, Michigan State University, East Lansing, MI 48824, USA
| | - Rémy Bigorne
- UMR EDB (Laboratoire Évolution et Diversité Biologique), CNRS 5174, IRD253, UPS; 118 route de Narbonne, F-31062 Toulouse, France
| | - Fernando M. Carvajal-Valleros
- Museo de Historia Natural Alcide d’Orbigny, Av. Potosí 1458, zona Queru Queru, Cochabamba, Estado Plurinacional de Bolivia
| | - Aaike De Wever
- Department of Freshwater Biology, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000 Brussels, Belgium
- Department of Biology, University of Ghent, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- Research Institute for Nature and Forrest (INBO), Havenlaan 88 bus 73, 1000 Brussels, Belgium
| | - R. G. Frederico
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Av. Antônio Carlos, 6627 Belo Horizonte, MG, Brazil
| | - Max Hidalgo
- Departamento de Ictiología, Museo de Historia Natural, Universidad Nacional Mayor San Marcos, Lima, Perú
| | - Bernard Hugueny
- UMR EDB (Laboratoire Évolution et Diversité Biologique), CNRS 5174, IRD253, UPS; 118 route de Narbonne, F-31062 Toulouse, France
| | - Fabien Leprieur
- UMR MARBEC (CNRS, IRD, IFREMER, UM), Université de Montpellier, Montpellier Cedex 5, France
| | - Mabel Maldonado
- Unidad de Limnología y Recursos Acuáticos, Universidad Mayor de San Simón, Calle Sucre y Parque La Torre s/n, Cochabamba, Bolivia
| | - Javier Maldonado-Ocampo
- Unidad de Ecología y Sistemática (UNESIS), Laboratorio de Ictiología, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Koen Martens
- Department of Freshwater Biology, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000 Brussels, Belgium
- Department of Biology, University of Ghent, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Hernan Ortega
- Departamento de Ictiología, Museo de Historia Natural, Universidad Nacional Mayor San Marcos, Lima, Perú
| | - Jaime Sarmiento
- Departamento de Ictiología, Museo Nacional de Historia Natural, La Paz, Bolivia
| | - Pablo A. Tedesco
- UMR EDB (Laboratoire Évolution et Diversité Biologique), CNRS 5174, IRD253, UPS; 118 route de Narbonne, F-31062 Toulouse, France
| | - Gislene Torrente-Vilara
- Universidade Federal de São Paulo, Instituto do Mar, Campus Baixada Santista, Rua Doutor Carvalho de Mendonça, 144, Encruzilhada, 11070-100 Santos, SP, Brazil
| | - Kirk O. Winemiller
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77840, USA
| | - Jansen Zuanon
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Avenida André Araújo, 2936, Petrópolis, 69067-375 Manaus, AM, Brazil
| |
Collapse
|
30
|
Sylvain F, Holland A, Audet‐Gilbert É, Luis Val A, Derome N. Amazon fish bacterial communities show structural convergence along widespread hydrochemical gradients. Mol Ecol 2019; 28:3612-3626. [DOI: 10.1111/mec.15184] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 07/13/2019] [Accepted: 07/15/2019] [Indexed: 12/30/2022]
Affiliation(s)
| | - Aleicia Holland
- Department of Ecology, Environment and Evolution School of Life Science La Trobe University Bundoora Vic. Australia
| | - Émie Audet‐Gilbert
- Institut de Biologie Intégrative et des Systèmes Université Laval Québec City QC Canada
| | - Adalberto Luis Val
- Laboratório de Ecofisiologia e Evolução Molecular Instituto Nacional de Pesquisas da Amazônia (INPA) Manaus Brazil
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes Université Laval Québec City QC Canada
| |
Collapse
|
31
|
Pires THS, Borghezan EA, Cunha SLR, Leitão RP, Pinto KS, Zuanon J. Sensory drive in colourful waters: morphological variation suggests combined natural and sexual selection in an Amazonian fish. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Tiago H S Pires
- Laboratório de Ecologia Comportamental e Evolutiva - LECE, Instituto Nacional de Pesquisas da Amazônia - INPA., Petrópolis, Manaus AM, Brazil
| | - Elio A Borghezan
- Laboratório de Ecologia Comportamental e Evolutiva - LECE, Instituto Nacional de Pesquisas da Amazônia - INPA., Petrópolis, Manaus AM, Brazil
- Wildlife Research Center of Kyoto University., Sakyo-ku, Kyoto, Japan
| | - Sergio L R Cunha
- Laboratório de Ecologia Comportamental e Evolutiva - LECE, Instituto Nacional de Pesquisas da Amazônia - INPA., Petrópolis, Manaus AM, Brazil
- Laboratório de Ecologia de Ecossistemas Aquáticos - LEEA, Universidade Federal do Ceará/UFC, Fortaleza CE, Brazil
| | - Rafael P Leitão
- Laboratório de Ecologia de Peixes, Departamento de Biologia Geral - ICB, Universidade Federal de Minas Gerais/UFMG, Pampulha, Belo Horizonte MG, Brazil
| | - Kalebe S Pinto
- Laboratório de Ecologia Comportamental e Evolutiva - LECE, Instituto Nacional de Pesquisas da Amazônia - INPA., Petrópolis, Manaus AM, Brazil
| | - Jansen Zuanon
- Laboratório de Ecologia Comportamental e Evolutiva - LECE, Instituto Nacional de Pesquisas da Amazônia - INPA., Petrópolis, Manaus AM, Brazil
| |
Collapse
|
32
|
Rodríguez-Zárate CJ, Sandoval-Castillo J, van Sebille E, Keane RG, Rocha-Olivares A, Urteaga J, Beheregaray LB. Isolation by environment in the highly mobile olive ridley turtle ( Lepidochelys olivacea) in the eastern Pacific. Proc Biol Sci 2019; 285:rspb.2018.0264. [PMID: 29720414 DOI: 10.1098/rspb.2018.0264] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/10/2018] [Indexed: 11/12/2022] Open
Abstract
Spatial and temporal scales at which processes modulate genetic diversity over the landscape are usually overlooked, impacting the design of conservation management practices for widely distributed species. We examine processes shaping population divergence in highly mobile species by re-assessing the case of panmixia in the iconic olive ridley turtle from the eastern Pacific. We implemented a biophysical model of connectivity and a seascape genetic analysis based on nuclear DNA variation of 634 samples collected from 27 nesting areas. Two genetically distinct populations largely isolated during reproductive migrations and mating were detected, each composed of multiple nesting sites linked by high connectivity. This pattern was strongly associated with a steep environmental gradient and also influenced by ocean currents. These findings relate to meso-scale features of a dynamic oceanographic interface in the eastern tropical Pacific (ETP) region, a scenario that possibly provides different cost-benefit solutions and selective pressures for sea turtles during both the mating and migration periods. We reject panmixia and propose a new paradigm for olive ridley turtles where reproductive isolation due to assortative mating is linked to its environment. Our study demonstrates the relevance of integrative approaches for assessing the role of environmental gradients and oceanographic currents as drivers of genetic differentiation in widely distributed marine species. This is relevant for the conservation management of species of highly mobile behaviour, and assists the planning and development of large-scale conservation strategies for the threatened olive ridley turtles in the ETP.
Collapse
Affiliation(s)
| | | | - Erik van Sebille
- Institute for Marine and Atmospheric Research, Utrecht University, 3584 CC, The Netherlands.,Grantham Institute and Department of Physics, Imperial College London, London SW7 2AZ, UK
| | - Robert G Keane
- Geographic Information Systems, Flinders University, Adelaide, South Adelaide 5001, Australia
| | - Axayácatl Rocha-Olivares
- Laboratorio de Ecología Molecular, Departamento de Oceanografía Biológica, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada Baja California 22860, Mexico
| | | | - Luciano B Beheregaray
- Molecular Ecology Laboratory, Flinders University, Adelaide, South Adelaide 5001, Australia
| |
Collapse
|
33
|
Oliveira JDA, Farias IP, Costa GC, Werneck FP. Model-based riverscape genetics: disentangling the roles of local and connectivity factors in shaping spatial genetic patterns of two Amazonian turtles with different dispersal abilities. Evol Ecol 2019. [DOI: 10.1007/s10682-019-09973-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
34
|
Klimova A, Ortega‐Rubio A, Vendrami DLJ, Hoffman JI. Genotyping by sequencing reveals contrasting patterns of population structure, ecologically mediated divergence, and long-distance dispersal in North American palms. Ecol Evol 2018; 8:5873-5890. [PMID: 29938100 PMCID: PMC6010798 DOI: 10.1002/ece3.4125] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 03/29/2018] [Indexed: 12/20/2022] Open
Abstract
Comparative studies can provide powerful insights into processes that affect population divergence and thereby help to elucidate the mechanisms by which contemporary populations may respond to environmental change. Furthermore, approaches such as genotyping by sequencing (GBS) provide unprecedented power for resolving genetic differences among species and populations. We therefore used GBS to provide a genomewide perspective on the comparative population structure of two palm genera, Washingtonia and Brahea, on the Baja California peninsula, a region of high landscape and ecological complexity. First, we used phylogenetic analysis to address taxonomic uncertainties among five currently recognized species. We resolved three main clades, the first corresponding to W. robusta and W. filifera, the second to B. brandegeei and B. armata, and the third to B. edulis from Guadalupe Island. Focusing on the first two clades, we then delved deeper by investigating the underlying population structure. Striking differences were found, with GBS uncovering four distinct Washingtonia populations and identifying a suite of loci associated with temperature, consistent with ecologically mediated divergence. By contrast, individual mountain ranges could be resolved in Brahea and few loci were associated with environmental variables, implying a more prominent role of neutral divergence. Finally, evidence was found for long-distance dispersal events in Washingtonia but not Brahea, in line with knowledge of the dispersal mechanisms of these palms including the possibility of human-mediated dispersal. Overall, our study demonstrates the power of GBS together with a comparative approach to elucidate markedly different patterns of genomewide divergence mediated by multiple effectors.
Collapse
Affiliation(s)
- Anastasia Klimova
- Centro de Investigaciones Biologicas del Noroeste S.C.La PazBaja California SurMexico
- Department of Animal BehaviourBielefeld UniversityBielefeldGermany
| | - Alfredo Ortega‐Rubio
- Centro de Investigaciones Biologicas del Noroeste S.C.La PazBaja California SurMexico
| | | | | |
Collapse
|
35
|
Pires THS, Borghezan EA, Machado VN, Powell DL, Röpke CP, Oliveira C, Zuanon J, Farias IP. Testing Wallace's intuition: water type, reproductive isolation and divergence in an Amazonian fish. J Evol Biol 2018; 31:882-892. [PMID: 29577482 DOI: 10.1111/jeb.13272] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 03/14/2018] [Accepted: 03/16/2018] [Indexed: 01/20/2023]
Abstract
Alfred Russel Wallace proposed classifying Amazon rivers based on their colour and clarity: white, black and clear water. Wallace also proposed that black waters could mediate diversification and yield distinct fish species. Here, we bring evidence of speciation mediated by water type in the sailfin tetra (Crenuchus spilurus), a fish whose range encompasses rivers of very distinct hydrochemical conditions. Distribution of the two main lineages concords with Wallace's water types: one restricted to the acidic and nutrient-poor waters of the Negro River (herein Rio Negro lineage) and a second widespread throughout the remaining of the species' distribution (herein Amazonas lineage). These lineages occur over a very broad geographical range, suggesting that despite occurring in regions separated by thousands of kilometres, individuals of the distinct lineages fail to occupy each other's habitats, hundreds of metres apart and not separated by physical barrier. Reproductive isolation was assessed in isolated pairs exposed to black-water conditions. All pairs with at least one individual of the lineage not native to black waters showed significantly lower spawning success, suggesting that the water type affected the fitness and contributed to reproductive isolation. Our results endorse Wallace's intuition and highlight the importance of ecological factors in shaping diversity of the Amazon fish fauna.
Collapse
Affiliation(s)
- Tiago H S Pires
- Laboratório de Ecologia Comportamental e Evolutiva/LECE, Instituto Nacional de Pesquisas da Amazônia/INPA, Manaus, AM, Brazil
| | - Elio A Borghezan
- Laboratório de Ecologia Comportamental e Evolutiva/LECE, Instituto Nacional de Pesquisas da Amazônia/INPA, Manaus, AM, Brazil
| | - Valeria N Machado
- Laboratório de Evolução e Genética Animal/LEGAL, Universidade Federal do Amazonas/UFAM, Manaus, AM, Brazil
| | - Daniel L Powell
- Department of Biology, Texas A&M University. TAMU, College Station, TX, USA
| | - Cristhiana P Röpke
- Departamento de Ciências Pesqueiras, Faculdade de Ciências Agrárias, Universidade Federal do Amazonas, Manaus, AM, Brazil
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Jansen Zuanon
- Laboratório de Ecologia Comportamental e Evolutiva/LECE, Instituto Nacional de Pesquisas da Amazônia/INPA, Manaus, AM, Brazil
| | - Izeni P Farias
- Laboratório de Evolução e Genética Animal/LEGAL, Universidade Federal do Amazonas/UFAM, Manaus, AM, Brazil
| |
Collapse
|
36
|
Jardim de Queiroz L, Torrente-Vilara G, Quilodran C, Rodrigues da Costa Doria C, Montoya-Burgos JI. Multifactorial genetic divergence processes drive the onset of speciation in an Amazonian fish. PLoS One 2017; 12:e0189349. [PMID: 29261722 PMCID: PMC5738069 DOI: 10.1371/journal.pone.0189349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/24/2017] [Indexed: 11/19/2022] Open
Abstract
Understanding the processes that drive population genetic divergence in the Amazon is challenging because of the vast scale, the environmental richness and the outstanding biodiversity of the region. We addressed this issue by determining the genetic structure of the widespread Amazonian common sardine fish Triportheus albus (Characidae). We then examined the influence, on this species, of all previously proposed population-structuring factors, including isolation-by-distance, isolation-by-barrier (the Teotônio Falls) and isolation-by-environment using variables that describe floodplain and water characteristics. The population genetics analyses revealed an unusually strong structure with three geographical groups: Negro/Tapajós rivers, Lower Madeira/Central Amazon, and Upper Madeira. Distance-based redundancy analyses showed that the optimal model for explaining the extreme genetic structure contains all proposed structuring factors and accounts for up to 70% of the genetic structure. We further quantified the contribution of each factor via a variance-partitioning analysis. Our results demonstrate that multiple factors, often proposed as individual drivers of population divergence, have acted in conjunction to divide T. albus into three genetic lineages. Because the conjunction of multiple long-standing population-structuring processes may lead to population reproductive isolation, that is, the onset of speciation, we suggest that the multifactorial population-structuring processes highlighted in this study could account for the high speciation rate characterising the Amazon Basin.
Collapse
Affiliation(s)
| | - Gislene Torrente-Vilara
- Department of Marine Sciences, Universidade Federal de São Paulo, Campus Baixada Santista, Santos/SP, Brazil
| | - Claudio Quilodran
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Switzerland
| | | | - Juan I. Montoya-Burgos
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Switzerland
- * E-mail:
| |
Collapse
|
37
|
The Role of Geographical and Ecological Factors on Population Divergence of the Neotropical otter Lontra longicaudis (Carnivora, Mustelidae). Evol Biol 2017. [DOI: 10.1007/s11692-017-9428-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
38
|
In the shadows: Phylogenomics and coalescent species delimitation unveil cryptic diversity in a Cerrado endemic lizard (Squamata: Tropidurus). Mol Phylogenet Evol 2017; 107:455-465. [DOI: 10.1016/j.ympev.2016.12.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 11/07/2016] [Accepted: 12/07/2016] [Indexed: 11/18/2022]
|
39
|
Escobedo-Morales LA, Mandujano S, Eguiarte LE, Rodríguez-Rodríguez MA, Maldonado JE. First phylogenetic analysis of Mesoamerican brocket deer Mazama pandora and Mazama temama (Cetartiodactyla: Cervidae) based on mitochondrial sequences: Implications for Neotropical deer evolution. Mamm Biol 2016. [DOI: 10.1016/j.mambio.2016.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|