scholarly journals Continental-scale gene flow prevents allopatric divergence of pelagic freshwater bacteria

2021 ◽  
Author(s):  
Matthias Hoetzinger ◽  
Alexandra Pitt ◽  
Andrea Huemer ◽  
Martin W Hahn
Keyword(s):  
Gene Flow ◽  
Regional Scale ◽  
Geographic Distance ◽  
Spatial Distance ◽  
Widespread Species ◽  
Continental Scale ◽  
Freshwater Bacteria ◽  
Wide Range ◽  
Allopatric Divergence ◽  
Open Question

Abstract Allopatric divergence is one of the principal mechanisms for speciation of macro-organisms. Microbes by comparison are assumed to disperse more freely and to be less limited by dispersal barriers. However, thermophilic prokaryotes restricted to geothermal springs have shown clear signals of geographic isolation, but robust studies on this topic for microbes with less strict habitat requirements are scarce. Furthermore, it has only recently been recognized that homologous recombination among conspecific individuals provides species coherence in a wide range of prokaryotes. Recombination barriers thus may define prokaryotic species boundaries, yet, the extent to which geographic distance between populations gives rise to such barriers is an open question. Here, we investigated gene flow and population structure in a widespread species of pelagic freshwater bacteria, Polynucleobacter paneuropaeus. Through comparative genomics of 113 conspecific strains isolated from freshwater lakes and ponds located across a North-South range of more than 3000 km, we were able to reconstruct past gene flow events. The species turned out to be highly recombinogenic as indicated by significant signs of gene transfer and extensive genome mosaicism. While genomic differences increased with spatial distance on a regional scale (< 170 km), such correlations were mostly absent on larger scales up to 3400 km. We conclude that allopatric divergence in European P. paneuropaeus is minor, and that effective gene flow across the sampled geographic range in combination with a high recombination efficacy maintains species coherence.

scholarly journals Conditions for mutation-order speciation

2010 ◽  
Vol 278 (1704) ◽  
pp. 399-407 ◽  
Author(s):  
Patrik Nosil ◽  
Samuel M. Flaxman
Keyword(s):  
Gene Flow ◽  
Initial Period ◽  
Simulation Models ◽  
Selective Advantage ◽  
Secondary Contact ◽  
Population Divergence ◽  
Divergent Natural Selection ◽  
Wide Range ◽  
Allopatric Divergence ◽  
Different Populations

Two models for speciation via selection have been proposed. In the well-known model of ‘ecological speciation’, divergent natural selection between environments drives the evolution of reproductive isolation. In a second ‘mutation-order’ model, different, incompatible mutations (alleles) fix in different populations adapting to the same selective pressure. How to demonstrate mutation-order speciation has been unclear, although it has been argued that it can be ruled out when gene flow occurs because the same, most advantageous allele will fix in all populations. However, quantitative examination of the interaction of factors influencing the likelihood of mutation-order speciation is lacking. We used simulation models to study how gene flow, hybrid incompatibility, selective advantage, timing of origination of new mutations and an initial period of allopatric differentiation affect population divergence via the mutation-order process. We find that at least some population divergence can occur under a reasonably wide range of conditions, even with moderate gene flow. However, strong divergence (e.g. fixation of different alleles in different populations) requires very low gene flow, and is promoted when (i) incompatible mutations have similar fitness advantages, (ii) less fit mutations arise slightly earlier in evolutionary time than more fit alternatives, and (iii) allopatric divergence occurs prior to secondary contact.

scholarly journals Spatial distance between sites of sampling associated with genetic variation among Neospora caninum in aborted bovine foetuses from northern Italy

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Luca Villa ◽  
Pavlo Maksimov ◽  
Christine Luttermann ◽  
Mareen Tuschy ◽  
Alessia L. Gazzonis ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Neospora Caninum ◽  
Geographic Distance ◽  
Rare Event ◽  
Northern Italy ◽  
Spatial Distance ◽  
Italian Regions ◽  
Bovine Abortion

Abstract Background Neospora caninum, a coccidian protozoan, represents an important cause of bovine abortion. Available N. caninum strains show considerable variation in vitro and in vivo, including different virulence in cattle. To which extent sexual recombination, which is possible in the intestines of domestic dogs and closely related carnivores as definitive hosts, contributes to this variation is not clear yet. Methods Aborted bovine foetuses were collected between 2015 and early 2019 from Italian Holstein Friesian dairy herds suffering from reproductive problems. A total of 198 samples were collected from 165 intensive farms located in Lombardy, northern Italy. N. caninum samples were subjected to multilocus-microsatellite genotyping using ten previously established microsatellite markers. In addition to our own data, those from a recent study providing data on five markers from other northern Italian regions were included and analysed. Results Of the 55 samples finally subjected to genotyping, 35 were typed at all or 9 out of 10 loci and their individual multilocus-microsatellite genotype (MLMG) determined. Linear regression revealed a statistically significant association between the spatial distance of the sampling sites with the genetic distance of N. caninum MLMGs (P < 0.001). Including data from this and a previous North Italian study into eBURST analysis revealed that several of N. caninum MLMGs from northern Italy separate into four groups; most of the samples from Lombardy clustered in one of these groups. Principle component analysis revealed similar clusters and confirmed MLMG groups identified by eBURST. Variations observed between MLMGs were not equally distributed over all loci, but predominantly observed in MS7, MS6A, or MS10. Conclusions Our findings confirm the concept of local N. caninum subpopulations. The geographic distance of sampling was associated with the genetic distance as determined by microsatellite typing. Results suggest that multi-parental recombination in N. caninum is a rare event, but does not exclude uniparental mating. More comprehensive studies on microsatellites in N. caninum and related species like Toxoplasma gondii should be undertaken, not only to improve genotyping capabilities, but also to understand possible functions of these regions in the genomes of these parasites.

scholarly journals Transferability Intercomparison: An Opportunity for New Insight on the Global Water Cycle and Energy Budget

2007 ◽  
Vol 88 (3) ◽  
pp. 375-384 ◽  
Author(s):  
E. S. Takle ◽  
J. Roads ◽  
B. Rockel ◽  
W. J. Gutowski ◽  
R. W. Arritt ◽  
...  
Keyword(s):  
Energy Budget ◽  
Climate Models ◽  
Climate Model ◽  
Water Cycle ◽  
Regional Climate ◽  
Climate Conditions ◽  
Continental Scale ◽  
Global Water Cycle ◽  
Wide Range ◽  
Global Water

A new approach, called transferability intercomparisons, is described for advancing both understanding and modeling of the global water cycle and energy budget. Under this approach, individual regional climate models perform simulations with all modeling parameters and parameterizations held constant over a specific period on several prescribed domains representing different climatic regions. The transferability framework goes beyond previous regional climate model intercomparisons to provide a global method for testing and improving model parameterizations by constraining the simulations within analyzed boundaries for several domains. Transferability intercomparisons expose the limits of our current regional modeling capacity by examining model accuracy on a wide range of climate conditions and realizations. Intercomparison of these individual model experiments provides a means for evaluating strengths and weaknesses of models outside their “home domains” (domain of development and testing). Reference sites that are conducting coordinated measurements under the continental-scale experiments under the Global Energy and Water Cycle Experiment (GEWEX) Hydrometeorology Panel provide data for evaluation of model abilities to simulate specific features of the water and energy cycles. A systematic intercomparison across models and domains more clearly exposes collective biases in the modeling process. By isolating particular regions and processes, regional model transferability intercomparisons can more effectively explore the spatial and temporal heterogeneity of predictability. A general improvement of model ability to simulate diverse climates will provide more confidence that models used for future climate scenarios might be able to simulate conditions on a particular domain that are beyond the range of previously observed climates.

Climate as the great equalizer of continental-scale erosion

2021 ◽  
Author(s):  
Gilby Jepson ◽  
Barbara Carrapa ◽  
Jack Gillespie ◽  
Ran Feng ◽  
Peter DeCelles ◽  
...  
Keyword(s):  
Central Asia ◽  
Regional Scale ◽  
Continental Scale ◽  
Active Tectonic ◽  
Tectonically Active ◽  
High Precipitation ◽  
Tectonic Boundaries ◽  
Great Equalizer ◽  
Tian Shan

&lt;p&gt;Central Asia is one of the most tectonically active and orographically diverse regions in the world and is the location of the highest topography on Earth resulting from major plate tectonic collisional events. Yet the role of tectonics versus climate on erosion remains one of the greatest debates of our time. We present the first regional scale analysis of 2526 published low-temperature thermochronometric dates from Central Asia spanning the Altai-Sayan, Tian Shan, Tibet, Pamir, and Himalaya. We compare these dates to tectonic processes (proximity to tectonic boundaries, crustal thickness, seismicity) and state-of-the-art paleoclimate simulations in order to constrain the relative influences of climate and tectonics on the topographic architecture and erosion of Central Asia. Predominance of pre-Cenozoic ages in much of the interior of central Asia suggests that significant topography was created prior to the India-Eurasia collision and implies limited subsequent erosion. Increasingly young cooling ages are associated with increasing proximity to active tectonic boundaries, suggesting a first-order control of tectonics on erosion. However, areas that have been sheltered from significant precipitation for extensive periods of time retain old cooling ages. This suggests that ultimately climate is the great equalizer of erosion. Climate plays a key role by enhancing erosion in areas with developed topography and high precipitation such as the Tian Shan and Altai-Sayan during the Mesozoic and the Himalaya during the Cenozoic. Older thermochronometric dates are associated with sustained aridity following more humid periods.&lt;/p&gt;

scholarly journals Abundance and Sources of Atmospheric Halocarbons in the Eastern Mediterranean

2017 ◽  
Author(s):  
Fabian Schoenenberger ◽  
Stephan Henne ◽  
Matthias Hill ◽  
Martin K. Vollmer ◽  
Giorgos Kouvarakis ◽  
...  
Keyword(s):  
Western Europe ◽  
Atmospheric Transport ◽  
Eastern Mediterranean ◽  
Stratospheric Ozone ◽  
Regional Scale ◽  
Top Down ◽  
Inversion Domain ◽  
Hfc 134A ◽  
Wide Range ◽  
Hfc 152A

Abstract. A wide range of anthropogenic halocarbons is released to the atmosphere, contributing to stratospheric ozone depletion and global warming. Using measurements of atmospheric abundances for the estimation of halocarbon emissions on the global and regional scale has become an important top-down tool for emission validation in the recent past, but many populated and developing areas of the world are only poorly covered by the existing atmospheric halocarbon measurement network. Here we present six months of continuous halocarbon observations from Finokalia on the island of Crete in the Eastern Mediterranean. The gases measured are the hydrofluorocarbons (HFCs), HFC-134a (CH2FCF3), HFC-125 (CHF2CF3), HFC-152a (CH3CHF2) and HFC-143a (CH3CF3), and the hydrochlorofluorocarbons (HCFCs), HCFC-22 (CHClF2) and HCFC-142b (CH3CClF2). The Eastern Mediterranean is home to 250 million inhabitants, consisting of a number of developed and developing countries, for which different emission regulations exist under the Kyoto and Montreal Protocols. Regional emissions of halocarbons were estimated with Lagrangian atmospheric transport simulations and a Bayesian inverse modelling system, using measurements at Finokalia in conjunction with those from Advanced Global Atmospheric Gases Experiment (AGAGE) sites at Mace Head (Ireland), Jungfraujoch (Switzerland) and Monte Cimone (Italy). Measured peak mole fractions at Finokalia showed generally smaller amplitudes for HFCs than at the European AGAGE sites, except periodic peaks of HFC-152a, indicating strong upwind sources. Higher peak mole fractions were observed for HCFCs, suggesting continued emissions from nearby developing regions such as Egypt and the Middle East. For 2013, the Eastern Mediterranean inverse emission estimates for the four analysed HFCs and the two HCFCs were 14.7 (6.7–23.3) Tg CO2eq yr-1 and 9.7 (4.3–15.7) Tg CO2eq yr-1, respectively. These emissions contributed 17.3 % (7.9–27.4 %) and 53 % (23.5–86%) to the total inversion domain, which covers the Eastern Mediterranean as well as Central and Western Europe. Greek bottom-up HFC emissions reported to the UNFCCC were much smaller than our top-down estimates, whereas for Turkey our estimates agreed with UNFCCC-reported values for HFC-125 and HFC-143a, but were much and slightly smaller for HFC-134a and HFC-152a, respectively. Sensitivity estimates suggest an improvement of the a posteriori emission estimates, i.e. a reduction of the uncertainties by 40–80 %, compared to an inversion using only the existing Central European AGAGE observations.

scholarly journals The Indo-Pacific Amalda (Neogastropoda, Olivoidea, Ancillariidae) revisited with molecular data, with special emphasis on New Caledonia

2020 ◽  
Author(s):  
Yuri I. Kantor ◽  
Magalie Castelin ◽  
Alexander Fedosov ◽  
Philippe Bouchet
Keyword(s):  
Gene Flow ◽  
Molecular Analysis ◽  
New Caledonia ◽  
Narrow Range ◽  
Regional Scale ◽  
Molecular Data ◽  
Shell Morphology ◽  
Species Limits ◽  
South West ◽  
Strait Of Malacca

In the ancillariid genus Amalda, the shell is character rich and 96 described species are currently treated as valid. Based on shell morphology, several subspecies have been recognized within Amalda hilgendorfi, with a combined range extending at depths of 150–750 m from Japan to the South-West Pacific. A molecular analysis of 78 specimens from throughout this range shows both a weak geographical structuring and evidence of gene flow at the regional scale. We conclude that recognition of subspecies (richeri Kilburn & Bouchet, 1988, herlaari van Pel, 1989, and vezzaroi Cossignani, 2015) within A. hilgendorfi is not justified. By contrast, hilgendorfi-like specimens from the Mozambique Channel and New Caledonia are molecularly segregated, and so are here described as new, as Amalda miriky sp. nov. and A. cacao sp. nov., respectively. The New Caledonia Amalda montrouzieri complex is shown to include at least three molecularly separable species, including A. allaryi and A. alabaster sp. nov. Molecular data also confirm the validity of the New Caledonia endemics Amalda aureomarginata, A. fuscolingua, A. bellonarum, and A. coriolis. The existence of narrow range endemics suggests that the species limits of Amalda with broad distributions, extending, e.g., from Japan to Taiwan (A. hinomotoensis) or even Indonesia, the Strait of Malacca, Vietnam and the China Sea (A. mamillata) should be taken with caution.

scholarly journals Genomic phylogeography of the White-crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes

2019 ◽  
Author(s):  
Jacob S. Berv ◽  
Leonardo Campagna ◽  
Teresa J. Feo ◽  
Ivandy Castro-Astor ◽  
Camila C. Ribas ◽  
...  
Keyword(s):  
Gene Flow ◽  
Distinct Species ◽  
Passerine Bird ◽  
Biological Species ◽  
Genetic Connectivity ◽  
Population Isolation ◽  
Continental Scale ◽  
The Andes ◽  
Areas Of Endemism ◽  
History Of

AbstractThe complex landscape history of the Neotropics has generated opportunities for population isolation and subsequent diversification that place this region among the most species-rich in the world. Detailed phylogeographic studies are required to uncover the biogeographic histories of Neotropical taxa, to identify evolutionary correlates of diversity, and to reveal patterns of genetic connectivity, disjunction, and potential differentiation among lineages from different areas of endemism. The White-crowned Manakin (Pseudopipra pipra) is a small suboscine passerine bird that is broadly distributed through the subtropical rainforests of Central America, the lower montane cloud forests of the Andes from Colombia to central Peru, the lowlands of Amazonia and the Guianas, and the Atlantic forest of southeast Brazil. Pseudopipra is currently recognized as a single, polytypic biological species. We studied the effect of the Neotropical landscape on genetic and phenotypic differentiation within this species using genomic data derived from double digest restriction site associated DNA sequencing (ddRAD), and mitochondrial DNA. Most of the genetic breakpoints we identify among populations coincide with physical barriers to gene flow previously associated with avian areas of endemism. The phylogenetic relationships among these populations imply a novel pattern of Andean origination for this group, with subsequent diversification into the Amazonian lowlands. Our analysis of genomic admixture and gene flow establishes a complex history of introgression between some western Amazonian populations. These reticulate processes confound our application of standard concatenated and coalescent phylogenetic methods and raise the question of whether a lineage in the western Napo area of endemism should be considered a hybrid species. Lastly, analysis of variation in vocal and plumage phenotypes in the context of our phylogeny supports the hypothesis that Pseudopipra is a species-complex composed of at least 8, and perhaps up to 17 distinct species which have arisen in the last ∼2.5 Ma.

scholarly journals Geography is more important than life history in the recent diversification of the tiger salamander complex

2021 ◽  
Vol 118 (17) ◽  
pp. e2014719118
Author(s):  
Kathryn M. Everson ◽  
Levi N. Gray ◽  
Angela G. Jones ◽  
Nicolette M. Lawrence ◽  
Mary E. Foley ◽  
...  
Keyword(s):  
Life History ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Tiger Salamander ◽  
Life History Variation ◽  
Mexican Axolotl ◽  
Population Genetic Differentiation ◽  
Wide Range ◽  
Lineage Divergence

The North American tiger salamander species complex, including its best-known species, the Mexican axolotl, has long been a source of biological fascination. The complex exhibits a wide range of variation in developmental life history strategies, including populations and individuals that undergo metamorphosis; those able to forego metamorphosis and retain a larval, aquatic lifestyle (i.e., paedomorphosis); and those that do both. The evolution of a paedomorphic life history state is thought to lead to increased population genetic differentiation and ultimately reproductive isolation and speciation, but the degree to which it has shaped population- and species-level divergence is poorly understood. Using a large multilocus dataset from hundreds of samples across North America, we identified genetic clusters across the geographic range of the tiger salamander complex. These clusters often contain a mixture of paedomorphic and metamorphic taxa, indicating that geographic isolation has played a larger role in lineage divergence than paedomorphosis in this system. This conclusion is bolstered by geography-informed analyses indicating no effect of life history strategy on population genetic differentiation and by model-based population genetic analyses demonstrating gene flow between adjacent metamorphic and paedomorphic populations. This fine-scale genetic perspective on life history variation establishes a framework for understanding how plasticity, local adaptation, and gene flow contribute to lineage divergence. Many members of the tiger salamander complex are endangered, and the Mexican axolotl is an important model system in regenerative and biomedical research. Our results chart a course for more informed use of these taxa in experimental, ecological, and conservation research.

scholarly journals Population Genetics of the Red Rock Lobster,  Jasus edwardsii

2021 ◽  
Author(s):  
◽  
Luke Thomas
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
New Zealand ◽  
Genetic Differentiation ◽  
Microsatellite Markers ◽  
Rocky Reef ◽  
Rock Lobster ◽  
Wide Range ◽  
Jasus Edwardsii ◽  
Polymorphic Microsatellite

<p>Understanding patterns of gene flow across a species range is a vital component of an effective fisheries management strategy. The advent of highly polymorphic microsatellite markers has facilitated the detection of fine-scale patterns of genetic differentiation at levels below the resolving power of earlier techniques. This has triggered the wide-spread re-examination of population structure for a number of commercially targeted species. The aims of thesis were to re-investigate patterns of gene flow of the red rock lobster Jasus edwardsii throughout New Zealand and across the Tasman Sea using novel microsatellite markers. Jasus edwardsii is a keystone species of subtidal rocky reef system and supports lucrative export markets in both Australia and New Zealand. Eight highly polymorphic microsatellite markers were developed from 454 sequence data and screened across a Wellington south coast population to obtain basic diversity indices. All loci were polymorphic with the number of alleles per locus ranging from 6-39. Observed and expected heterozygosity ranged from 0.563-0.937 and 0.583-0.961, respectively. There were no significant deviations from Hardy-Weinberg equilibrium following standard Bonferroni corrections. The loci were used in a population analysis of J. edwardsii that spanned 10 degrees of latitude and stretched 3,500 km across the South Pacific. The analysis rejected the null-hypothesis of panmixia based on earlier mDNA analysis and revealed significant population structure (FST=0.011, RST=0.028) at a wide range of scales. Stewart Island was determined to have the highest levels of genetic differentiation of all populations sampled suggesting a high degree of reproductive isolation and self-recruitment. This study also identified high levels of asymmetric gene flow from Australia to New Zealand indicating a historical source-sink relationship between the two countries. Results from the genetic analysis were consistent with results from oceanographic dispersal models and it is likely that the genetic results reflect historical and contemporary patterns of Jasus edwardsii dispersal and recruitment throughout its range.</p>

scholarly journals Evolved phenological cueing strategies show variable responses to climate change

2018 ◽  
Author(s):  
Collin B. Edwards ◽  
Louie Yang
Keyword(s):  
Climate Change ◽  
Climatic Conditions ◽  
Similar Response ◽  
Climate Data ◽  
Global Pattern ◽  
Continental Scale ◽  
Fitness Consequences ◽  
Wide Range ◽  
Correlation Structures ◽  
Phenological Shifts

AbstractSeveral studies have documented a global pattern of phenological advancement that is consistent with ongoing climate change. However, the magnitude of these phenological shifts is highly variable across taxa and locations. This variability of phenological responses has been difficult to explain mechanistically. To examine how the evolution of multi-trait cueing strategies could produce variable responses to climate change, we constructed a model in which organisms evolve strategies that integrate multiple environmental cues to inform anticipatory phenological decisions. We simulated the evolution of phenological cueing strategies in multiple environments, using historic climate data from 78 locations in North America and Hawaii to capture features of climatic correlation structures in the real world. Organisms in our model evolved diverse strategies that were spatially autocorrelated across locations on a continental scale, showing that similar strategies tend to evolve in similar climates. Within locations, organisms often evolved a wide range of strategies that showed similar response phenotypes and fitness outcomes under historical conditions. However, these strategies responded differently to novel climatic conditions, with variable fitness consequences. Our model shows how the evolution of phenological cueing strategies can explain observed variation in phenological shifts and unexpected responses to climate change.

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