Population dynamics of Amazonian floodplain forest species support spatial variation on genetic diversity but not range expansions through time

Aim: We tested if historical demographic changes of populations occurring on the floodplains of a major Amazon Basin tributary could be associated with range expansions from upper and middle sections of the river, following the establishment of widespread river-created environments during the Late Pleistocene and Holocene. Location: Solimoes River, Western Amazon, South America Taxon: Myrmoborus lugubris, Thamnophilus cryptoleucus and Myrmotherula assimilis Methods: We analyzed thousands of UltraConserved Elements to explore spatial patterns of genetic diversity and connectivity between individuals. Range expansions were tested with alternative methods. We quantified habitat preference for the analyzed species in order to test if the occupation of dynamic habitats could predict spatial patterns of genetic diversity. Results: Our study did not support shared population range expansions related to historical regionalized changes in habitat availability. We found considerable variation in the spatial distribution of the genetic diversity between studied taxa, and that species with higher levels of specialization to dynamic environments have a more heterogeneous distribution of genetic diversity and reduced levels of gene flow across space. Main conclusions: Our results suggest that demographic expansions along the Solimoes River might be linked to geographic homogeneous oscillation in the distribution of floodplain environments, promoting effective population size changes but not range expansion. We found that habitat specificity might be a good predictor of population connectivity along the Amazonian floodplains.

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When ecological marginality is not geographically peripheral: exploring genetic predictions of the centre-periphery hypothesis in the endemic plantLilium pomponium

PeerJ ◽

10.7717/peerj.11039 ◽

2021 ◽

Vol 9 ◽

pp. e11039

Author(s):

Gabriele Casazza ◽

Carmelo Macrì ◽

Davide Dagnino ◽

Maria Guerrina ◽

Marianick Juin ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Environmental Gradients ◽

Population Connectivity ◽

Peripheral Populations ◽

Effective Population ◽

Population Isolation ◽

Genetic Traits ◽

Range Dynamics ◽

Center Periphery

BackgroundQuantifying variation of genetic traits over the geographical range of species is crucial for understanding the factors driving their range dynamics. The center-periphery hypothesis postulates, and many studies support, the idea that genetic diversity decreases and genetic differentiation increases toward the geographical periphery due to population isolation. The effects of environmental marginality on genetic variation has however received much less attention.MethodsWe tested the concordance between geographical and environmental gradients and the genetic predictions of center-periphery hypothesis for endemicLilium pomponiumin the southern Alps.ResultsWe found little evidence for concordance between genetic variation and both geographical and environmental gradients. Although the prediction of increased differentiation at range limits is met, genetic diversity does not decrease towards the geographical periphery. Increased differentiation among peripheral populations, that are not ecologically marginal, may be explained by a decrease in habitat availability that reduces population connectivity. In contrast, a decrease of genetic diversity along environmental but not geographical gradients may be due to the presence of low quality habitats in the different parts of the range of a species that reduce effective population size or increase environmental constraints. As a result, environmental factors may affect population dynamics irrespective of distance from the geographical center of the range. In such situations of discordance between geographical and environmental gradients, the predictions of decreasing genetic diversity and increasing differentiation toward the geographical periphery may not be respected.

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Evolutionary genetics of small populations

10.1093/oso/9780198783398.003.0002 ◽

2017 ◽

Author(s):

Richard Frankham ◽

Jonathan D. Ballou ◽

Katherine Ralls ◽

Mark D. B. Eldridge ◽

Michele R. Dudash ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Evolutionary Genetics ◽

Small Population ◽

Small Populations ◽

Effective Population ◽

Genetic Management ◽

Evolutionary Genetic ◽

Loss Of Genetic Diversity ◽

Number Of Individuals

Genetic management of fragmented populations involves the application of evolutionary genetic theory and knowledge to alleviate problems due to inbreeding and loss of genetic diversity in small population fragments. Populations evolve through the effects of mutation, natural selection, chance (genetic drift) and gene flow (migration). Large outbreeding, sexually reproducing populations typically contain substantial genetic diversity, while small populations typically contain reduced levels. Genetic impacts of small population size on inbreeding, loss of genetic diversity and population differentiation are determined by the genetically effective population size, which is usually much smaller than the number of individuals.

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Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection

Genetics Selection Evolution ◽

10.1186/s12711-021-00644-z ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Emmanuel A. Lozada-Soto ◽

Christian Maltecca ◽

Duc Lu ◽

Stephen Miller ◽

John B. Cole ◽

...

Keyword(s):

Genetic Diversity ◽

Beef Cattle ◽

Genomic Selection ◽

Inbreeding Depression ◽

Growth Traits ◽

Effective Population ◽

Angus Cattle ◽

Genomic Inbreeding ◽

Chromosome Segments ◽

The Impact

Abstract Background While the adoption of genomic evaluations in livestock has increased genetic gain rates, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased inbreeding may affect fitness and decrease the mean performance for economically important traits, such as fertility and growth in beef cattle, with the age of inbreeding having a possible effect on the magnitude of inbreeding depression. The purpose of this study was to determine changes in genetic diversity as a result of the implementation of genomic selection in Angus cattle and quantify potential inbreeding depression effects of total pedigree and genomic inbreeding, and also to investigate the impact of recent and ancient inbreeding. Results We found that the yearly rate of inbreeding accumulation remained similar in sires and decreased significantly in dams since the implementation of genomic selection. Other measures such as effective population size and the effective number of chromosome segments show little evidence of a detrimental effect of using genomic selection strategies on the genetic diversity of beef cattle. We also quantified pedigree and genomic inbreeding depression for fertility and growth. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain in both sexes. We also measured the impact of the age of inbreeding and found that recent inbreeding had a larger depressive effect on growth than ancient inbreeding. Conclusions In this study, we sought to quantify and understand the possible consequences of genomic selection on the genetic diversity of American Angus cattle. In both sires and dams, we found that, generally, genomic selection resulted in decreased rates of pedigree and genomic inbreeding accumulation and increased or sustained effective population sizes and number of independently segregating chromosome segments. We also found significant depressive effects of inbreeding accumulation on economically important growth traits, particularly with genomic and recent inbreeding.

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Population structure and genetic diversity of non-native aoudad populations

Scientific Reports ◽

10.1038/s41598-021-91678-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Sunčica Stipoljev ◽

Toni Safner ◽

Pavao Gančević ◽

Ana Galov ◽

Tina Stuhne ◽

...

Keyword(s):

Genetic Diversity ◽

Control Region ◽

Effective Population ◽

The Czech Republic ◽

Mitochondrial Dna Control Region ◽

Mountain Ranges ◽

Spanish Populations ◽

Microsatellite Alleles ◽

Shared Alleles ◽

Number Of Individuals

AbstractThe aoudad (Ammotragus lervia Pallas 1777) is an ungulate species, native to the mountain ranges of North Africa. In the second half of the twentieth century, it was successfully introduced in some European countries, mainly for hunting purposes, i.e. in Croatia, the Czech Republic, Italy, and Spain. We used neutral genetic markers, the mitochondrial DNA control region sequence and microsatellite loci, to characterize and compare genetic diversity and spatial pattern of genetic structure on different timeframes among all European aoudad populations. Four distinct control region haplotypes found in European aoudad populations indicate that the aoudad has been introduced in Europe from multiple genetic sources, with the population in the Sierra Espuña as the only population in which more than one haplotype was detected. The number of detected microsatellite alleles within all populations (< 3.61) and mean proportion of shared alleles within all analysed populations (< 0.55) indicates relatively low genetic variability, as expected for new populations funded by a small number of individuals. In STRUCTURE results with K = 2–4, Croatian and Czech populations cluster in the same genetic cluster, indicating joined origin. Among three populations from Spain, Almeria population shows as genetically distinct from others in results, while other Spanish populations diverge at K = 4. Maintenance of genetic diversity should be included in the management of populations to sustain their viability, specially for small Czech population with high proportion of shared alleles (0.85) and Croatian population that had the smallest estimated effective population size (Ne = 5.4).

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Small population size and low genomic diversity have no effect on fitness in experimental translocations of a wild fish

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2019.1989 ◽

2019 ◽

Vol 286 (1916) ◽

pp. 20191989 ◽

Cited By ~ 1

Author(s):

M. C. Yates ◽

E. Bowles ◽

D. J. Fraser

Keyword(s):

Genetic Diversity ◽

Body Size ◽

Population Size ◽

Brook Trout ◽

Habitat Degradation ◽

Species Conservation ◽

Empirical Work ◽

Genomic Diversity ◽

Effective Population ◽

Isolated Populations

Little empirical work in nature has quantified how wild populations with varying effective population sizes and genetic diversity perform when exposed to a gradient of ecologically important environmental conditions. To achieve this, juvenile brook trout from 12 isolated populations or closed metapopulations that differ substantially in population size and genetic diversity were transplanted to previously fishless ponds spanning a wide gradient of ecologically important variables. We evaluated the effect of genome-wide variation, effective population size ( N e ), pond habitat, and initial body size on two fitness correlates (survival and growth). Genetic variables had no effect on either fitness correlate, which was determined primarily by habitat (pond temperature, depth, and pH) and initial body size. These results suggest that some vertebrate populations with low genomic diversity, low N e , and long-term isolation can represent important sources of variation and are capable of maintaining fitness in, and ultimately persisting and adapting to, changing environments. Our results also reinforce the paramount importance of improving available habitat and slowing habitat degradation for species conservation.

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The history of genetic diversity and effective population size of an isolated Microtus oeconomus population on Kis Balaton

Mammalian Biology ◽

10.1007/s42991-021-00199-y ◽

2021 ◽

Author(s):

Veronika Sládkovičová ◽

Dávid Žiak ◽

Peter Miklós ◽

András Gubányi ◽

Győző Horváth

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

Effective Population ◽

Microtus Oeconomus ◽

History Of

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Fragmentation effects and genetic diversity of the key semidecidual forest species Metrodorea nigra in Southwestern Brazil

Genetics and Molecular Research ◽

10.4238/2015.april.15.15 ◽

2015 ◽

Vol 14 (2) ◽

pp. 3509-3524 ◽

Cited By ~ 5

Author(s):

R.M. Moraes Filho ◽

F. Bonifácio-Anacleto ◽

A.L. Alzate-Marin

Keyword(s):

Genetic Diversity ◽

Forest Species ◽

Metrodorea Nigra

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Low genetic diversity in the endangered Taxus yunnanensis following a population bottleneck, a low effective population size and increased inbreeding

Silvae Genetica ◽

10.1515/sg-2016-0008 ◽

2016 ◽

Vol 65 (1) ◽

pp. 59-66 ◽

Cited By ~ 3

Author(s):

Y. C. Miao ◽

Z. J. Zhang ◽

J. R. Su

Keyword(s):

Genetic Diversity ◽

Habitat Fragmentation ◽

Population Size ◽

Effective Population Size ◽

Spatial Genetic Structure ◽

Population Bottleneck ◽

Effective Population ◽

Taxus Yunnanensis ◽

Low Genetic Diversity ◽

Two Populations

Abstract Taxus yunnanensis, which is an endangered tree that is considered valuable because it contains the effective natural anticancer metabolite taxol and heteropolysaccharides, has long suffered from severe habitat fragmentation. In this study, the levels of genetic diversity in two populations of 136 individuals were analyzed based on eleven polymorphic microsatellite loci. Our results suggested that these two populations were characterized by low genetic diversity (NE = 2.303/2.557; HO = 0.168/0.142; HE = 0.453/0.517), a population bottleneck, a low effective population size (Ne = 7/9), a high level of inbreeding (FIS = 0.596/0.702), and a weak, but significant spatial genetic structure (Sp = 0.001, b = −0.001*). Habitat fragmentation, seed shadow overlap and limited seed and pollen dispersal and potential selfing may have contributed to the observed gene tic structure. The results of the present study will enable development of practical conservation measures to effectively conserve the valuable genetic resources of this endangered plant.

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Genetic variation in native and farmed populations of Tambaqui (Colossoma macropomum) in the Brazilian Amazon: regional discrepancies in farming systems

Anais da Academia Brasileira de Ciências ◽

10.1590/0001-376520130007 ◽

2013 ◽

Vol 85 (4) ◽

pp. 1439-1447 ◽

Cited By ~ 8

Author(s):

Jonas Aguiar ◽

Horacio Schneider ◽

Fatima Gomes ◽

Jeferson Carneiro ◽

Simoni Santos ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Dna Sequences ◽

Amazon Basin ◽

Farming Systems ◽

Wild Populations ◽

The West ◽

Colossoma Macropomum ◽

Breeding Stock ◽

History Of

The tambaqui, Colossoma macropomum, is the most popular fish species used for aquaculture in Brazil but there is no study comparing genetic variation among native and farmed populations of this species. In the present study, we analyzed DNA sequences of the mitochondrial DNA to evaluate the genetic diversity among two wild populations, a fry-producing breeding stock, and a sample of fish farm stocks, all from the region of Santarém, in the west of the Brazilian state of Pará. Similar levels of genetic diversity were found in all the samples and surprisingly the breeding stock showed expressive representation of the genetic diversity registered on wild populations. These results contrast considerably with those of the previous study of farmed stocks in the states of Amapá, Pará, Piauí, and Rondônia, which recorded only two haplotypes, indicating a long history of endogamy in the breeding stocks used to produce fry. The results of the two studies show two distinct scenarios of tambaqui farming in the Amazon basin, which must be better evaluated in order to guarantee the successful expansion of this activity in the region, and the rest of Brazil, given that the tambaqui and its hybrids are now farmed throughout the country.

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