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Guzmán S, Giudicelli GC, Turchetto C, Bombarely A, Freitas LB. Neutral and outlier single nucleotide polymorphisms disentangle the evolutionary history of a coastal Solanaceae species. Mol Ecol 2022; 31:2847-2864. [PMID: 35332594 DOI: 10.1111/mec.16441] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 03/11/2022] [Accepted: 03/16/2022] [Indexed: 11/30/2022]
Abstract
Speciation begins with the isolation of some individuals or subpopulations due to drivers promoting a diverging genetic distribution. Such isolation may occur, followed by different processes and pressures. Isolation-by-distance (IBD), isolation-by-adaptation (IBA), and isolation-by-colonization (IBC) have been recognized as the main divergence patterns. Still, it is not easy to distinguish which one is the main pattern as each one may act at different points in time or even simultaneously. Using an extensive genome coverage from a Petunia species complex with coastal and inland distribution and multiple analytical approaches on population genomics and phylogeography, we showed a complex interplay between neutral and selective forces acting on the divergence process. We found 18,887 SNPs potentially neutral and 924 potentially under selection (outlier) loci. All analyses pointed that each subspecies displays its own genetic component and evolutionary history. We suggested plausible ecologic drivers for such divergence in a southernmost South Atlantic coastal plain in Brazil and Uruguay and identified a connection between adaptation and environment heterogeneity.
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Affiliation(s)
- Sebastián Guzmán
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Giovanna C Giudicelli
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Caroline Turchetto
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Department of Botany, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Loreta B Freitas
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Pirani RM, Tonini JFR, Thomaz AT, Napoli MF, Encarnação LC, Knowles LL, Werneck FP. Deep Genomic Divergence and Phenotypic Admixture of the Treefrog Dendropsophus elegans (Hylidae: Amphibia) Coincide With Riverine Boundaries at the Brazilian Atlantic Forest. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.765977] [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
The Atlantic Forest (AF) domain is one of the Earth’s biodiversity hotspots, known for its high levels of species diversity and endemism. Factors related to palaeoenvironmental dynamics, such as the establishment of vegetational refugia and river basins, have different impacts on biological communities and biodiversity patterns in this domain. Here, we sample genome-wide RADseq data from a widespread treefrog (Dendropsophus elegans), inhabiting natural and human-impacted ecosystems at the Brazilian AF to test the impact of riverine boundaries and climatic refugia on population structure and diversification. We estimate divergence times and migration rate across identified genetic breaks related to the rivers Doce, Paraíba do Sul, Ribeira de Iguape, and Paraguaçu, known to represent barriers to gene flow for other AF endemic species, and test the role of climatic refugia. Finally, we investigate the impact of spatio-temporal population history on morphological variation in this species. We recovered a phylogeographic history supporting three distinct clades separated into two geographically structured populations, corresponding to the north and south of AF. In addition, we identified an admixture zone between north and south populations in the latitude close to the Doce River. Our findings support a pattern of isolation-by-distance and the existence of a secondary contact zone between populations, which might have been promoted by gene flow during population expansion. Further, we found support for models considering migration parameters for all the tested rivers with different population divergence times. Based on the species history and the AF palaeoenvironmental dynamics, we corroborate the role of forest refugia impacting population structure for this species through recent range expansion after the Last Glacial Maximum (LGM). The Doce and Paraíba do Sul Rivers coincide with the main genetic breaks, suggesting they might also have played a role in the diversification processes. Finally, despite finding subtle correlations for phenotypic data among different populations, variation is not strongly detectable and does not seem associated with speciation-level processes that could warrant taxonomic changes. Such results can be explained by phenotypic plasticity of the evaluated traits and by recent divergence times, where there has been insufficient time and weak selective pressures to accumulate enough phenotypic differences.
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Peek RA, O'Rourke SM, Miller MR. Flow modification associated with reduced genetic health of a river‐breeding frog,
Rana boylii. Ecosphere 2021. [DOI: 10.1002/ecs2.3496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Ryan A. Peek
- Center for Watershed Sciences University of California Davis California95616USA
| | - Sean M. O'Rourke
- Department of Animal Science University of California Davis California95616USA
| | - Michael R. Miller
- Department of Animal Science University of California Davis California95616USA
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Damasceno RP, Carnaval AC, Sass C, Sousa Recoder R, Moritz C, Trefaut Rodrigues M. Geographic restriction, genetic divergence, and morphological disparity in the Brazilian Atlantic Forests: Insights from Leposoma lizards (Gymnophthalmidae, Squamata). Mol Phylogenet Evol 2020; 154:106993. [PMID: 33148523 DOI: 10.1016/j.ympev.2020.106993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 09/01/2020] [Accepted: 09/28/2020] [Indexed: 10/23/2022]
Abstract
Lineage differentiation, long-term persistence, and range limitation promote high levels of phylogenetic and phylogeographic endemisms and likely underlie the abundant morphologically cryptic diversity observed in the Brazilian Atlantic Forests (AF). We explore lineage differentiation and range restriction in the AF and ask if genetic divergence and morphological disparity are correlated by integrating coalescent-based species delimitation, molecular phylogenetic, and morphological analyses in the lizard genus Leposoma. We present the first species tree for Leposoma and of their tribe, the Ecpleopodini. The analyses are based on the largest dataset ever assembled for Leposoma in terms of number of species (all represented), genetic markers (12 loci), and geographic coverage (~2,500 km). The exercise allows us to robustly delimit species within the genus and phylogeographic lineages within all species. We find support for the monophyly of the genus and for the recognition of a yet undescribed species around the Baía de Todos-os-Santos, in the state of Bahia; this form is distinct from all other congeners, both genetically and morphologically. We find that L. baturitensis, from the northeastern state of Ceará, is basal to the genus - and sister to a clade of six species restricted to the AF across the eastern coast of Brazil. Relationships within this coastal clade are ((((L. annectans, Leposoma sp.), L. scincoides), L. puk) (L. nanodactylus, L. sinepollex)). Phylogenetic and phylogeographic analyses, together with precise distribution data, allowed us to update the ranges of species and phylogeographic lineages. We reveal pervasive geographic restriction of divergent lineages in Leposoma at and below species level and discuss how forest refuges and rivers might have contributed to it. We find that morphological disparity lags behind genetic divergence in the genus because although they are correlated, the first accumulates at a much slower rate than the latter. We hope to encourage new studies in the area of AF north of the Doce river; phylogeographic sampling in that region has been much less common relative to southern sites, yet it may hold the key to several important processes defining biodiversity patterns in eastern Brazil. This appears to specially apply to processes underlying geographic restriction of morphologically cryptic, yet genetic divergent lineages, as the case of Leposoma.
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Affiliation(s)
- Roberta P Damasceno
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, trav. 14, n. 321, Cidade Universitária, São Paulo, SP 05508-090, Brazil; Museum of Vertebrate Zoology, University of California, Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA.
| | - Ana Carolina Carnaval
- Department of Biology, City College of New York and the Biology Program at the Graduate Center of CUNY, 160 Convent Avenue, Marshak Life Science Building J-526, New York, NY 10031, USA.
| | - Chodon Sass
- Museum of Vertebrate Zoology, University of California, Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA; University and Jepson Herbaria, University of California, Berkeley, 1001 Valley Life Sciences Building, Berkeley, CA 94720, USA.
| | - Renato Sousa Recoder
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, trav. 14, n. 321, Cidade Universitária, São Paulo, SP 05508-090, Brazil
| | - Craig Moritz
- Museum of Vertebrate Zoology, University of California, Berkeley, 3101 Valley Life Sciences Building, Berkeley, CA 94720, USA; Division of Ecology and Evolution, Research School of Biology, and Centre for Biodiversity Analysis, The Australian National University, 46 Sullivans Creek Road, Acton, ACT 2601, Australia.
| | - Miguel Trefaut Rodrigues
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, trav. 14, n. 321, Cidade Universitária, São Paulo, SP 05508-090, Brazil.
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Almeida JPFA, Thomé MTC, Sturaro MJ, Pereira RJ, Mott T. The relative role of glacial refugia and longstanding barriers in the diversification of a fossorial squamate. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1783716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- João P. F. A. Almeida
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, AL 57072-970, Brazil
| | - Maria Tereza C. Thomé
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, AL 57072-970, Brazil
| | - Marcelo J. Sturaro
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Av. Professor Artur Riedel, 275, Jardim Eldorado, Diadema, São Paulo, CEP 09972-270, Brazil
| | - Ricardo J. Pereira
- Division of Evolutionary Biology, Faculty of Biology II, Ludwig- Maximilians-Universität München, Grosshaderner Strasse 2, München, 82152, Germany
| | - Tamí Mott
- Laboratório de Biologia Integrativa, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, AL 57072-970, Brazil
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Multilocus phylogeny of Paratelmatobiinae (Anura: Leptodactylidae) reveals strong spatial structure and previously unknown diversity in the Atlantic Forest hotspot. Mol Phylogenet Evol 2020; 148:106819. [PMID: 32289449 DOI: 10.1016/j.ympev.2020.106819] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 02/15/2020] [Accepted: 04/01/2020] [Indexed: 11/21/2022]
Abstract
The Brazilian Atlantic Forest harbors high levels of anuran diversity and endemism, including several taxa restricted to small geographic ranges. Here, we provide a multilocus phylogeny for Paratelmatobiinae, a leptodactylid subfamily composed of small-ranged species distributed in the Brazilian Atlantic Forest and in the campo rupestre ecosystem. We performed Bayesian inference and maximum likelihood analyses using three mitochondrial and five nuclear markers, and a matrix comprising a broad taxonomic sampling. We then delimitated independently evolving lineages within the group. We recovered Paratelmatobiinae and each of its four genera as monophyletic and robustly supported. Five putatively new species included in our analyses were unambiguously supported in the phylogenetic trees and delimitation analyses. We also recovered other deeply divergent and geographically structured lineages within the four genera of Paratelmatobiinae. Our estimation of divergence times indicates that diversification in the subfamily began in the Eocene and continued until the Pleistocene. We discuss possible scenarios of diversification for the four genera of Paratelmatobiinae, and outline the implications of our findings for taxonomy and conservation.
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Qian ZH, Li Y, Li MW, He YX, Li JX, Ye XF. Molecular Phylogeography Analysis Reveals Population Dynamics and Genetic Divergence of a Widespread Tree Pterocarya stenoptera in China. Front Genet 2019; 10:1089. [PMID: 31737056 PMCID: PMC6838215 DOI: 10.3389/fgene.2019.01089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 10/09/2019] [Indexed: 01/19/2023] Open
Abstract
The geological events, past climatic fluctuations, and river systems played key roles in the spatial distribution, population dynamics, and genetic differentiation of species. In this work, we selected Pterocarya stenoptera, a widespread tree species in China, to test the roles of these factors. Four noncoding spacers, eight microsatellite (simple sequence repeat) markers, and species distribution modeling were used to examine the phylogeographical pattern of P. stenoptera. Based on chloroplast DNA data, populations of P. stenoptera were clearly clustered into three groups. The divergence time of these groups fell into the stage of the Qinghai–Tibet Movement, 1.7–2.6 Ma. For simple sequence repeat data, only one western marginal population YNYB could be separated from other populations, whereas other populations were mixed together. Our results indicated that the environmental heterogeneity resulting from the Qinghai–Tibet movement might be response for this genetic divergence. The climatic fluctuations in the Pleistocene did not cause the substantial range shift of P. stenoptera, while the fluctuations affected its population size. Moreover, we also confirmed the river systems did not act as channels or barrier of dispersal for P. stenoptera.
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Affiliation(s)
- Zhi-Hao Qian
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Yong Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Ming-Wan Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Yan-Xia He
- School of Life Sciences, Henan University, Kaifeng, China
| | - Jia-Xin Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Xiao-Fan Ye
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
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Lompo D, Vinceti B, Konrad H, Gaisberger H, Geburek T. Phylogeography of African Locust Bean (Parkia biglobosa) Reveals Genetic Divergence and Spatially Structured Populations in West and Central Africa. J Hered 2019; 109:811-824. [PMID: 30247720 PMCID: PMC6208456 DOI: 10.1093/jhered/esy047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 09/20/2018] [Indexed: 01/03/2023] Open
Abstract
The evolutionary history of African savannah tree species is crucial for the management of their genetic resources. In this study, we investigated the phylogeography of Parkia biglobosa and its modeled distribution under past and present climate conditions. This tree species is very valued and widespread in West Africa, providing edible and medicinal products. A large sample of 1610 individuals from 84 populations, distributed across 12 countries in Western and Central Africa, were genotyped using 8 nuclear microsatellites. Individual-based assignments clearly distinguished 3 genetic clusters, extreme West Africa (EWA), center of West Africa (CWA), and Central Africa (CA). Overall, estimates of genetic diversity were moderate to high, with lower values for populations in EWA (allelic richness after rarefaction [AR] = 6.4, expected heterozygosity [HE] = 0.78, and observed heterozygosity [HO] = 0.7) and CA (AR = 5.9, HE = 0.67, and HO = 0.61) compared with populations in CWA (AR = 7.3, HE = 0.79, and HO = 0.75). The overall population differentiation was found to be moderate (FST = 0.09). A highly significant isolation by distance pattern was detected, with a marked phylogeographic signature suggesting possible effects of past climate and geographic barriers to migration. Modeling the potential distribution of the species showed a contraction during the last glaciations followed by expansion events. The exploratory approximate Bayesian computation conducted suggests a best-supported scenario in which the cluster CWA traced back to the ancestral populations and a first split between EWA and CWA took place about 160000 years before present (BP), then a second split divided CA and CWA, about 100000 years BP. However, our genetic data do not enable us to conclusively distinguish among a few alternative possible scenarios.
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Affiliation(s)
- Djingdia Lompo
- Centre National de Semences Forestières, Ouagadougou, Burkina Faso
| | | | - Heino Konrad
- Austrian Research and Training Centre for Forests, Department of Forest Genetics, Vienna, Austria
| | | | - Thomas Geburek
- Austrian Research and Training Centre for Forests, Department of Forest Genetics, Vienna, Austria
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Bruschi DP, Peres EA, Lourenço LB, Bartoleti LFDM, Sobral-Souza T, Recco-Pimentel SM. Signature of the Paleo-Course Changes in the São Francisco River as Source of Genetic Structure in Neotropical Pithecopus nordestinus (Phyllomedusinae, Anura) Treefrog. Front Genet 2019; 10:728. [PMID: 31475035 PMCID: PMC6702341 DOI: 10.3389/fgene.2019.00728] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 07/11/2019] [Indexed: 11/13/2022] Open
Abstract
Historical processes that have interrupted gene flow between distinct evolutionary lineages have played a fundamental role in the evolution of the enormous diversity of species found in the Neotropical region. Numerous studies have discussed the role of geographic barriers and Pleistocene forest refugia in the diversification of the region's biodiversity. In the present study, we investigated the relative contribution of these different factors to the evolutionary history of Pithecopus nordestinus, a Neotropical tree frog, which is amply distributed in the Brazilian Atlantic Forest and adjacent areas of the Caatinga biome. We used an extensive sample and multilocus DNA sequences to provide an overview of the intraspecific genetic diversity of P. nordestinus, characterize historical diversification patterns, and identify possible phylogenetic splits. We tested different scenarios of diversification based on Pleistocene Refugia and river barrier models using approximate Bayesian computation (ABC) and ecological niche modeling (ENM). The phylogenetic approach indicate the occurrence of processes of phylogeographic divergence in both time and space, related to historical shifts in the course of the São Francisco River during Plio-Pleistocene period, resulting in two principal, highly divergent clades. The ABC model provided strong statistical support for this scenario, confirming the hypothesis that the São Francisco River acted as an effective geographical barrier during vicariant events in the evolutionary history of P. nordestinus. We believe that the climatic changes that occurred during the Pleistocene also played a secondary role in the genetic signatures identified, reinforcing the divergence of populations isolated by physical barriers. These findings reinforce the conclusion that the two models of diversification (geographic barriers and refugia) are not mutually exclusive in the Neotropical domain but may interact extensively during the diversification of species on a regional scale.
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Affiliation(s)
| | - Elen Arroyo Peres
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Luciana Bolsoni Lourenço
- Department of Structural and Functional Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | | | - Thadeu Sobral-Souza
- Spatial Ecology and Conservation Lab (LEEC), São Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
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Backes A, Mäder G, Turchetto C, Segatto AL, Fregonezi JN, Bonatto SL, Freitas LB. How diverse can rare species be on the margins of genera distribution? AOB PLANTS 2019; 11:plz037. [PMID: 31391895 PMCID: PMC6677564 DOI: 10.1093/aobpla/plz037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 07/08/2019] [Indexed: 06/10/2023]
Abstract
Different genetic patterns have been demonstrated for narrowly distributed taxa, many of them linking rarity to evolutionary history. Quite a few species in young genera are endemics and have several populations that present low variability, sometimes attributed to geographical isolation or dispersion processes. Assessing the genetic diversity and structure of such species may be important for protecting them and understanding their diversification history. In this study, we used microsatellite markers and plastid sequences to characterize the levels of genetic variation and population structure of two endemic and restricted species that grow in isolated areas on the margin of the distribution of their respective genera. Plastid and nuclear diversities were very low and weakly structured in their populations. Evolutionary scenarios for both species are compatible with open-field expansions during the Pleistocene interglacial periods and genetic variability supports founder effects to explain diversification. At present, both species are suffering from habitat loss and changes in the environment can lead these species towards extinction.
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Affiliation(s)
- Alice Backes
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Geraldo Mäder
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Caroline Turchetto
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Ana Lúcia Segatto
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Jeferson N Fregonezi
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Sandro L Bonatto
- Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Loreta B Freitas
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
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12
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Sosa V, Loera I, Angulo DF, Vásquez-Cruz M, Gándara E. Climate change and conservation in a warm North American desert: effect in shrubby plants. PeerJ 2019; 7:e6572. [PMID: 30867993 PMCID: PMC6409089 DOI: 10.7717/peerj.6572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 02/05/2019] [Indexed: 11/20/2022] Open
Abstract
Background Deserts are biologically rich habitats with a vast array of animals and plants adapted to xeric conditions, and most deserts are among the planet’s last remaining areas of total wilderness. Among North American deserts, the Chihuahuan Desert has the highest levels of diversity and endemism. To understand the effect of future climate change on plants distributed in this arid land and propose effective conservation planning, we focused on five endemic shrubby species that characterize the Chihuahuan Desert and used an integrative approach. Methods Ecological niche-based modeling, spatial genetics and ecological resistance analyses were carried out to identify the effect of global warming on the studied five shrubby species. Key areas that need to be preserved were identified taking into account the existing protected areas within the Chihuahuan Desert. Results The extent of future distribution will vary among these species, and on average expansion will occur in the western part of the Chihuahuan Desert. For most species low environmental resistance to gene flow was predicted, while higher future resistance was predicted for one species that would lead to increased population isolation. The highest haplotype diversity was identified in three hotspots. Based on future suitability of habitat and in the haplotype diversity we suggest preserving two hotspots of genetic diversity in the Sierra Madre Oriental, located in areas without protection. The third hotspot was detected in the well preserved Tehuacán-Cuicatlán Man and Biosphere Reserve. Conclusion Global climate change will have an effect in arid adapted plants, favoring expansion in the western of the Chihuahuan Desert however negatively affecting others with high ecological resistance disrupting gene flow. Two hotspots of genetic diversity in the Sierra Madre Oriental should be protected.
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Affiliation(s)
- Victoria Sosa
- Biología Evolutiva, Instituto de Ecología AC, Xalapa, Veracruz, Mexico
| | - Israel Loera
- Biología Evolutiva, Instituto de Ecología AC, Xalapa, Veracruz, Mexico
| | - Diego F Angulo
- Biología Evolutiva, Instituto de Ecología AC, Xalapa, Veracruz, Mexico
| | | | - Etelvina Gándara
- Biología Evolutiva, Instituto de Ecología AC, Xalapa, Veracruz, Mexico.,Facultad de Ciencias Biológicas, Benemérita Universidad Autónoma de Puebla, Mexico
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13
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Cryptic diversity in Brazilian endemic monkey frogs (Hylidae, Phyllomedusinae, Pithecopus) revealed by multispecies coalescent and integrative approaches. Mol Phylogenet Evol 2019; 132:105-116. [DOI: 10.1016/j.ympev.2018.11.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 11/29/2018] [Accepted: 11/30/2018] [Indexed: 11/22/2022]
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14
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Low population genetic differentiation in two Tamarix species (Tamarix austromongolica and Tamarix chinensis) along the Yellow River. Genetica 2018; 147:13-22. [DOI: 10.1007/s10709-018-0047-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 11/16/2018] [Indexed: 10/27/2022]
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Barros MJF, Diniz-Filho JAF, Freitas LB. Ecological drivers of plant genetic diversity at the southern edge of geographical distributions: Forestal vines in a temperate region. Genet Mol Biol 2018; 41:318-326. [PMID: 29668009 PMCID: PMC5913715 DOI: 10.1590/1678-4685-gmb-2017-0031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 06/12/2017] [Indexed: 11/21/2022] Open
Abstract
The Tropical Niche Conservatism hypothesis is one of the most relevant theories to explain why tropical diversity is high, although the mechanisms underlying this hypothesis require further clarification. A possible research avenue to address the underlying mechanisms includes determining population-level processes associated with such a hypothesis, in particular by trying to identify how adaptation may occur in extreme niche conditions at the edges of species ranges. However, the determinants of molecular diversity at the edges of geographical distributions of tropical taxa are still poorly known. Here we assessed which environmental variables determine diversity in nuclear and plastid genetic markers for populations of four Passiflora species in the southern limit of their geographical distributions. Climatic factors can drive genetic diversity, and their importance varies according to the marker. The primary predictors are variables representing higher temperatures during cold periods of the year and higher precipitation during dry periods. We concluded that, although these species are present in colder areas at the edge of their range, Tropical Niche Conservatism acts as a restraining force on genetic diversity in southern populations of Passiflora.
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Affiliation(s)
- Michel J F Barros
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - Loreta B Freitas
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Salzano FM. Remembering the past - studies on evolution done by the genetics group at Universidade Federal do Rio Grande do Sul (UFRGS). Genet Mol Biol 2018; 41:181-188. [PMID: 29583152 PMCID: PMC5913724 DOI: 10.1590/1678-4685-gmb-2017-0049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 02/27/2017] [Indexed: 11/22/2022] Open
Abstract
After a brief introduction about the factors that are involved in science development, and world and Brazilian evolutionary genetics, the studies developed in Porto Alegre in this area were reviewed. Four periods in the development of this group were distinguished: (a) Origins and first expansion (1949-1961); (b) Second expansion (1962-1988); (c) Third expansion (1989-2001); and (d) The last 15 years (2002-present). The international Porto Alegre Biological Evolution Workshops (PABEWs), with five biannual events from 2007 o 2015, were also mentioned. The final message stressed the importance of the maintenance of this and other Brazilian groups of research through adequate finance and recognition.
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Affiliation(s)
- Francisco M Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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17
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Santos BF, Scherrer MV, Loss AC. Neither barriers nor refugia explain genetic structure in a major biogeographic break: phylogeography of praying mantises in the Brazilian Atlantic Forest. Mitochondrial DNA A DNA Mapp Seq Anal 2018. [PMID: 29514536 DOI: 10.1080/24701394.2018.1445242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The Atlantic Forest is one of the world's top biodiversity hotspots, but the diversification processes of its biota are still poorly known, with competing models attributing dominant roles to either Quaternary climatic changes or geographic barriers. Many studies identify the Doce river as a major phylogeographic break, but the reasons for this phenomenon are highly debated. Here we test the predictions of the refugial and barrier models for a common species of praying mantis, Miobantia fuscata, focusing in the areas immediately south and north of the Doce river. Our analyses show high intraspecific genetic diversity, deep coalescence times and no evidence for recent population expansion. Phylogeographic structure is inconsistent with a refugial hypothesis. Significant gene flow between northern and southern populations also conflicts with a strong role for geographic barriers. This study highlights the need for considering invertebrate taxa to infer recent landscape changes, and points towards a more complex picture of genetic diversification in the Atlantic Forest.
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Affiliation(s)
- Bernardo F Santos
- a Department of Entomology , National Museum of Natural History , Washington, DC , USA
| | - Marcus V Scherrer
- b Universidade Federal do Espírito Santo , Vitória , ES , Brazil.,c Instituto Federal do Espírito Santo , Santa Teresa , ES , Brazil
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18
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Liang HY, Feng ZP, Pei B, Li Y, Yang XT. Demographic expansion of two Tamarix species along the Yellow River caused by geological events and climate change in the Pleistocene. Sci Rep 2018; 8:60. [PMID: 29311687 PMCID: PMC5758526 DOI: 10.1038/s41598-017-19034-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 12/20/2017] [Indexed: 11/13/2022] Open
Abstract
The geological events and climatic fluctuations during the Pleistocene played important roles in shaping patterns of species distribution. However, few studies have evaluated the patterns of species distribution that were influenced by the Yellow River. The present work analyzed the demography of two endemic tree species that are widely distributed along the Yellow River, Tamarix austromongolica and Tamarix chinensis, to understand the role of the Yellow River and Pleistocene climate in shaping their distribution patterns. The most common chlorotype, chlorotype 1, was found in all populations, and its divergence time could be dated back to 0.19 million years ago (Ma). This dating coincides well with the formation of the modern Yellow River and the timing of Marine Isotope Stages 5e-6 (MIS 5e-6). Bayesian reconstructions along with models of paleodistribution revealed that these two species experienced a demographic expansion in population size during the Quaternary period. Approximate Bayesian computation analyses supported a scenario of expansion approximately from the upper to lower reaches of the Yellow River. Our results provide support for the roles of the Yellow River and the Pleistocene climate in driving demographic expansion of the populations of T. austromongolica and T. chinensis. These findings are useful for understanding the effects of geological events and past climatic fluctuations on species distribution patterns.
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Affiliation(s)
- Hong-Yan Liang
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China.,Sanmenxia Polytechnic, Sanmenxia, 472000, China
| | - Zhi-Pei Feng
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Bing Pei
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yong Li
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xi-Tian Yang
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China.
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19
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Franco FF, Jojima CL, Perez MF, Zappi DC, Taylor N, Moraes EM. The xeric side of the Brazilian Atlantic Forest: The forces shaping phylogeographic structure of cacti. Ecol Evol 2017; 7:9281-9293. [PMID: 29187968 PMCID: PMC5696397 DOI: 10.1002/ece3.3458] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/07/2017] [Accepted: 08/11/2017] [Indexed: 01/15/2023] Open
Abstract
In order to investigate biogeographic influences on xeric biota in the Brazilian Atlantic Forest (BAF), a biodiversity hotspot, we used a monophyletic group including three cactus taxa as a model to perform a phylogeographic study: Cereus fernambucensis subsp. fernambucensis, C. fernambucensis subsp. sericifer, and C. insularis. These cacti are allopatric and grow in xeric habitats along BAF, including isolated granite and gneiss rock outcrops (Inselbergs), sand dune vegetation (Restinga forest), and the rocky shore of an oceanic archipelago (islands of Fernando de Noronha). The nucleotide information from nuclear gene phytochrome C and plastid intergenic spacer trnS-trnG was used to perform different approaches and statistical analyses, comprising population structure, demographic changes, phylogenetic relationships, and biogeographic reconstruction in both spatial and temporal scales. We recovered four allopatric population groups with highly supported branches in the phylogenetic tree with divergence initiated in the middle Pleistocene: southern distribution of C. fernambucensis subsp. fernambucensis, northern distribution of C. fernambucensis subsp. fernambucensis together with C. insularis, southern distribution of C. fernambucensis subsp. sericifer, and northern distribution of C. fernambucensis subsp. sericifer. Further, the results suggest that genetic diversity of population groups was strongly shaped by an initial colonization event from south to north followed by fragmentation. The phylogenetic pattern found for C. insularis is plausible with peripatric speciation in the archipelago of Fernando de Noronha. To explain the phylogeographic patterns, the putative effects of both climatic and sea level changes as well as neotectonic activity during the Pleistocene are discussed.
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Affiliation(s)
- Fernando Faria Franco
- Departamento de BiologiaCentro de Ciências Humanas e BiológicasUniversidade Federal de São CarlosSorocabaBrazil
| | - Cecília Leiko Jojima
- Departamento de BiologiaCentro de Ciências Humanas e BiológicasUniversidade Federal de São CarlosSorocabaBrazil
| | - Manolo Fernandez Perez
- Departamento de BiologiaCentro de Ciências Humanas e BiológicasUniversidade Federal de São CarlosSorocabaBrazil
| | - Daniela Cristina Zappi
- Museu Paraense Emilio GoeldiCoord. Botânica/Instituto Tecnológico ValeBelém do ParáBrazil
| | | | - Evandro Marsola Moraes
- Departamento de BiologiaCentro de Ciências Humanas e BiológicasUniversidade Federal de São CarlosSorocabaBrazil
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20
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Time scaled phylogeography and demography of Bradypus torquatus (Pilosa: Bradypodidae). Glob Ecol Conserv 2017. [DOI: 10.1016/j.gecco.2017.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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