Hidden diversity within the broadly distributed Amazonian giant monkey frog (Phyllomedusa bicolor: Phyllomedusidae)

Abstract Phyllomedusa bicolor is a large-sized nocturnal tree frog found in tropical rainforests throughout much of the Amazonian region of Brazil, Colombia, Bolivia, Peru, Venezuela, and the Guianas. Very little is known about P. bicolor genetic diversity and genealogical history of its natural populations. Here, using a sampling design that included populations covering most of its distributional range, we investigated the spatial distribution of genetic variability of this species, and we tested the hypothesis that P. bicolor is composed of deeply structured genetic groups, constituting more than one lineage across the Brazilian Amazonia. The results suggested two main lineages in two geographic mega-regions: Western and Eastern Amazonia, the latter consisting of three population groups distributed in the Guiana and Brazilian Shields. The present findings have implications to taxonomy, to understanding the processes that lead to diversification, and to defining strategies of conservation and medicinal use of the species.

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The effect of population bottleneck size and selective regime on genetic diversity and evolvability in bacteria

10.1101/726158 ◽

2019 ◽

Author(s):

Tanita Wein ◽

Tal Dagan

Keyword(s):

Genetic Diversity ◽

Genetic Drift ◽

Evolutionary Dynamics ◽

Natural Populations ◽

Population Bottleneck ◽

Population Bottlenecks ◽

High Genetic Diversity ◽

Temperature Regimes ◽

Consequent Reduction ◽

History Of

AbstractPopulation bottlenecks leading to a drastic reduction of the population size are common in the evolutionary dynamics of natural populations; their occurrence is known to have implications for genome evolution due to genetic drift, the consequent reduction in genetic diversity and the rate of adaptation. Nevertheless, an empirical characterization of the effect of population bottleneck size on evolutionary dynamics of bacteria is currently lacking. Here we show that selective conditions have a stronger effect on the evolutionary history of bacteria in comparison to genetic drift following population bottlenecks. We evolved Escherichia coli populations under three different population bottlenecks (small, medium, large) in two temperature regimes (37°C and 20°C). We find a high genetic diversity in the large in comparison to the small bottleneck size. Nonetheless, the cold temperature led to reduced genetic diversity in all bottleneck sizes, hence, the temperature has a stronger effect on the genetic diversity in comparison to the bottleneck size. A comparison of the fitness gain among the evolved populations reveals a similar pattern where the temperature has a significant effect on the fitness. Our study demonstrates that population bottlenecks are an important determinant of the evolvability in bacteria; their consequences depend on the selective conditions and are best understood via their effect on the standing genetic variation.

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European Vintage tomatoes galore: a result of farmers combinatorial assorting/swapping of a few diversity rich loci

10.1101/2021.10.26.465840 ◽

2021 ◽

Author(s):

Jose Blanca ◽

Clara Pons ◽

Javier Montero-Pau ◽

David Sanchez-Matarredona ◽

Peio Ziarsolo ◽

...

Keyword(s):

Genetic Diversity ◽

Morphological Traits ◽

Balancing Selection ◽

Genotyping By Sequencing ◽

Polymorphic Loci ◽

Comprehensive Collection ◽

Low Genetic Diversity ◽

Genetic Groups ◽

History Of ◽

Modern Varieties

A comprehensive collection of 1,254 tomato accessions corresponding to European heirlooms and landraces, together with modern varieties, early domesticates and wild relatives, were analyzed by genotyping by sequencing. A continuous genetic gradient between the vintage and modern varieties was observed. European vintage tomatoes displayed very low genetic diversity, with only 298 loci out of 64,943 variants being polymorphic at the 95% threshold. European vintage tomatoes could be classified in several genetic groups. Two main clusters consisting of Spanish and Italian accessions showed a higher genetic diversity than the rest varieties, suggesting that these regions might be independent secondary centers of diversity and with a different history. Other varieties seem to be the result of a more recent complex pattern of migrations and hybridizations among the European regions. Several polymorphic loci were associated in a GWAS with fruit morphological traits in the European vintage collection, and the corresponding alleles were found to contribute to the distinctive phenotypic characteristic of the genetic varietal groups. The few highly polymorphic loci associated with morphological traits in an otherwise diversity-poor genome suggests a history of balancing selection, in which tomato farmers maintained the morphological variation by applying a high selective pressure within different varietal types.

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Genetic causes and consequences of the breakdown of self-incompatibility: case studies in the Brassicaceae

Genetics Research ◽

10.1017/s0016672307008907 ◽

2008 ◽

Vol 90 (1) ◽

pp. 47-60 ◽

Cited By ~ 25

Author(s):

BARBARA K. MABLE

Keyword(s):

Genetic Diversity ◽

Demographic History ◽

Natural Populations ◽

Genetic Load ◽

Self Incompatibility ◽

Negative Consequences ◽

Recessive Mutations ◽

Mating System Evolution ◽

History Of ◽

Selective Forces

SummaryThe genetic consequences of inbreeding is a subject that has received thorough theoretical attention and has been of interest to empirical biologists since the time of Darwin. Particularly for species with genetically controlled mechanisms to promote outcrossing (self-incompatibility or SI systems), it is expected that high levels of genetic load should accumulate through sheltering of deleterious recessive mutations. Nevertheless, transitions to selfing are common across angiosperms, which suggests that the potentially negative consequences of reduced heterozygosity and genetic diversity are balanced by other factors, such as reproductive assurance. This mini-review focuses on empirical research in the Brassicaceae to emphasize some of the genetic consequences of shifts to inbreeding in terms of mechanisms for loss of SI, changes in genetic diversity following loss of SI, and inbreeding depression in relation to outcrossing history. Despite the long history of theoretical attention, there are still some surprisingly large gaps in our understanding in each of these areas. Rather than providing a complete overview, examples are drawn predominantly from published and emerging data from Arabidopsis thaliana and its relatives to highlight recent progress and remaining questions. We are currently on the brink of major breakthroughs in understanding due both to advances in sequencing technology and a shift in focus from crop plants to natural populations, where critical factors such as population structure, phylogeography, demographic history, partial compatibility and individual variation can be taken into account when investigating the nature of the selective forces regulating mating system evolution.

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Low genetic diversity and inbreeding depression in Queensland Koalas

Wildlife Research ◽

10.1071/wr9930177 ◽

1993 ◽

Vol 20 (2) ◽

pp. 177 ◽

Cited By ~ 29

Author(s):

JMW Wilmer ◽

A Melzer ◽

F Carrick ◽

C Moritz

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Inbreeding Depression ◽

Natural Populations ◽

Small Population ◽

Phascolarctos Cinereus ◽

Low Genetic Diversity ◽

History Of ◽

Biased Sex Ratio ◽

Two Populations

The amount of genetic variation in two natural populations of Queensland koalas (Phascolarctos cinereus adustus) was assessed by analysis of mitochondrial DNA. Levels and any adverse effects of inbreeding (inbreeding depression) were estimated from the pedigree of a well-characterised captive colony. Genetic diversity of mitochondrial DNA was found to be exceedingly low both within and between the two populations, but the variation detected was found to be strongly structured geographically. Inbreeding levels in the captive colony were moderate to high yet the only apparent evidence of inbreeding depression was a male-biased sex ratio. There was no evidence for decreased juvenile survivorship or growth rate with inbreeding. Because of the limited data it would be premature to conclude that koalas are relatively resistant to the effects of inbreeding. However, we suggest the hypothesis that koalas have a history of small population size, resulting in reduced susceptibility to inbreeding depression.

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The effect of population bottleneck size and selective regime on genetic diversity and evolvability in bacteria

Genome Biology and Evolution ◽

10.1093/gbe/evz243 ◽

2019 ◽

Author(s):

Tanita Wein ◽

Tal Dagan

Keyword(s):

Genetic Diversity ◽

Evolutionary Dynamics ◽

Natural Populations ◽

Population Bottleneck ◽

Population Bottlenecks ◽

High Genetic Diversity ◽

Temperature Regimes ◽

Consequent Reduction ◽

History Of

Abstract Population bottlenecks leading to a drastic reduction of the population size are common in the evolutionary dynamics of natural populations; their occurrence is known to have implications for genome evolution due to genetic drift, the consequent reduction in genetic diversity and the rate of adaptation. Nevertheless, an empirical characterization of the effect of population bottleneck size on evolutionary dynamics of bacteria is currently lacking. Here we show that selective conditions have a stronger effect on the evolutionary history of bacteria in comparison to population bottlenecks. We evolved Escherichia coli populations under three different population bottleneck sizes (small, medium, large) in two temperature regimes (37 °C and 20 °C). We find a high genetic diversity in the large in comparison to the small bottleneck size. Nonetheless, the cold temperature led to reduced genetic diversity regardless the bottleneck size, hence, the temperature has a stronger effect on the genetic diversity in comparison to the bottleneck size. A comparison of the fitness gain among the evolved populations reveals a similar pattern where the temperature has a significant effect on the fitness. Our study demonstrates that population bottlenecks are an important determinant of bacterial evolvability; their consequences depend on the selective conditions and are best understood via their effect on the standing genetic variation.

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Genetic diversity and structure in natural populations of Cajui from Brazilian Cerrado

Bioscience Journal ◽

10.14393/bj-v37n0a2021-53974 ◽

2021 ◽

Vol 37 ◽

pp. e37080

Author(s):

Maria Fernanda Da Costa Gomes ◽

Artemisa Nazaré Costa Borges ◽

Giovana Sarah Sales Batista ◽

Gizele De Andrade Luz ◽

Maria Edileide Alencar Oliveira ◽

...

Keyword(s):

Genetic Diversity ◽

Natural Populations ◽

Small Animal ◽

Floral Biology ◽

Diversity Indices ◽

Conservation Strategies ◽

Brazilian Cerrado ◽

Genetic Groups ◽

Genetic Diversity And Structure ◽

High Gene

Cajui (Anacardium spp.) is a native fruit tree (small cashew) of the Brazilian Cerrado and possesses the potential for commercialization. However, cajui exploitation occurs exclusively through extractivism in the absence of conservation strategies. The lack of conservation strategies may lead to a decrease in genetic diversity of Anacardium. In this work, the genetic diversity and population structure of three natural populations in Sete Cidades National Park (PNSC; PI, Brazil) were assessed using ISSR analysis of 56 cajui accessions and two A. occidentale accessions (outgroup) from Pacajus (CE, Brazil). A total of 112 markers were obtained, 93 (83.04%) of which were polymorphic. The diversity indices of these populations indicated moderate levels of genetic diversity. According to AMOVA, 96.17% of the genetic variability lay within populations, with low genetic differentiation among populations (ΦST = 0.03828). Furthermore, STRUCTURE analysis indicated the existence of four connected genetic groups. The findings show that the individuals from the three collection sites did not represent different subpopulations, likely due to the high gene flow (Nm = 6.7) favored by the floral biology of Anacardium, pollinators and small-animal seed dispersers. This research identifies genetically divergent individuals (C-03, C-05, C-22, C-26, C-34 and C-39), which should be considered priority individuals for conservation and can inform conservation programs for Anacardium spp.

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Genetic Diversity and Demographic History of the Shaggy Soft-Haired Mouse Abrothrix hirta (Cricetidae; Abrotrichini)

Frontiers in Genetics ◽

10.3389/fgene.2021.642504 ◽

2021 ◽

Vol 12 ◽

Author(s):

Lourdes Valdez ◽

Guillermo D’Elía

Keyword(s):

Genetic Diversity ◽

Demographic History ◽

Population Expansion ◽

Principal Component ◽

Tierra Del Fuego ◽

Local Fauna ◽

Recent Population Expansion ◽

Genetic Groups ◽

History Of ◽

Species Specific

Genetic information on species can inform decision making regarding conservation of biodiversity since the response of organisms to changing environments depend, in part, on their genetic makeup. Territories of central-southern Chile and Argentina have undergone a varying degree of impact during the Quaternary, where the response of local fauna and flora was rather species-specific. Here, we focus on the sigmodontine rodent Abrothrix hirta, distributed from 35° S in Chile and Argentina to northern Tierra del Fuego. Based on 119,226 transcriptome-derived SNP loci from 46 individuals of A. hirta, we described the geographic distribution of the genetic diversity of this species using a maximum likelihood tree, principal component and admixture analyses. We also addressed the demographic history of the main intraspecific lineages of A. hirta using GADMA. We found that A. hirta exhibited four allopatric intraspecific lineages. Three main genetic groups were identified by a Principal Component Analysis and by Ancestry analysis. The demographic history of A. hirta was characterized by recent population stability for populations at the northernmost part of the range, while southern populations experienced a recent population expansion.

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Diversity and Genetic Structure Inferred with Microsatellites in Natural Populations of Pseudotsuga menziesii (Mirb.) Franco (Pinaceae) in the Central Region of Mexico

Forests ◽

10.3390/f10020101 ◽

2019 ◽

Vol 10 (2) ◽

pp. 101 ◽

Cited By ~ 2

Author(s):

Paulina Montiel Castelán ◽

Moisés Cortés-Cruz ◽

Ma. Mendoza-Castillo ◽

Serafín Cruz-Izquierdo ◽

Javier López-Upton ◽

...

Keyword(s):

Genetic Diversity ◽

Pseudotsuga Menziesii ◽

Central Region ◽

Natural Populations ◽

The United States ◽

Effective Number ◽

Genetic Studies ◽

Genetic Groups ◽

Expected Heterozygosity ◽

Mexican Populations

The amount and structure of the genetic diversity in Mexican populations of Pseudotsuga menziesii (Mirb.) Franco, is almost unknown, since most genetic studies have been carried out on populations from Canada and the United States. Here, we applied a set of 12 microsatellite markers to 12 populations (234 trees) from the central region of Mexico in order to determine values of genetic diversity and differentiation. Seventy-three different alleles were identified: an average number of alleles per locus (Na) of 6.083, effective number of alleles (Ne) of 2.039, observed heterozygosity (Ho) of 0.229, and expected heterozygosity (Ht) of 0.417. Genetic differentiation was high: the coefficient of differentiation (θ) was 0.270, while the coefficient of structure (Φst) was 0.278. Bayesian analysis identified two genetic groups in central Mexico. The PCoA and the dendrogram were in concordance with the two genetic groups. The results of the analysis of molecular variance (AMOVA) indicate that genetic variation exists mainly within populations (72.149%). Therefore, conservation efforts should focus on as many individuals within populations as possible, to maintain this variation.

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Hidden Rice Diversity in the Guianas

10.1101/562769 ◽

2019 ◽

Author(s):

Tinde van Andel ◽

Margret Veltman ◽

Alice Bertin ◽

Harro Maat ◽

Thomas Polime ◽

...

Keyword(s):

Genetic Diversity ◽

Oryza Glaberrima ◽

Crop Varieties ◽

Geographic Structure ◽

External Pressures ◽

History Of ◽

Rice Improvement ◽

Modern Breeding ◽

The Guianas ◽

Rice Diversity

AbstractTraditional crop varieties are an important source of genetic diversity for crop adaptation and modern breeding. Landraces of Asian (Oryza sativa) and African (Oryza glaberrima) rice have been well studied on the continents where they were domesticated. However, their history of cultivation in northern South America is poorly understood. Here we reveal the rice diversity that is maintained by Maroons, descendants of enslaved Africans who fled to the interior forests of the Guianas ca. 300 years ago. We interviewed subsistence farmers who practice shifting cultivation along the Maroni and Lawa rivers that form the natural border between French Guiana and Suriname, and used ethnobotanical and morphological methods to identify around 50 varieties, of which 15 were previously undocumented. The genetic origin of these varieties was explored using the Angiosperms-353 universal probe set. Despite the large distances between sites and relative inaccessibility of the area, phenotypic and genetic diversity did not display any geographic structure, which is consistent with knowledge of seed exchange among members of the same ethnolinguistic group. Although improved US cultivars were introduced in Maroon villages in the 1940s, these have not displaced the traditional landraces, which are cherished for their taste and nutritious qualities and for their importance in Maroon spiritual life. The unique agricultural and ritual practices of Maroons confirm their role as custodians of rice diversity, a role that is currently under threat from external pressures and encroaching globalization. We expect that the rice diversity uncovered in this study represents only a fraction of the total diversity in the Guianas and may constitute a large untapped resource that holds promise for future rice improvement. Further efforts to inventory and preserve these landraces will help to protect a precious cultural heritage and local food security.

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Current plantation practices have negligible genetic effects on planted dipterocarps in the tropical rainforest

Silvae Genetica ◽

10.1515/sg-2013-0035 ◽

2013 ◽

Vol 62 (1-6) ◽

pp. 292-299 ◽

Cited By ~ 1

Author(s):

A. Izuno ◽

S. Indrioko ◽

Widiyatno Widiyatno ◽

E. Prasetyo ◽

Kasmujiono Kasmujiono ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Sustainable Management ◽

Tropical Rainforest ◽

Sustainable Use ◽

Natural Populations ◽

Tropical Rainforests ◽

Natural Forests ◽

Commercially Important ◽

Shorea Leprosula

Abstract Dipterocarp trees are ecologically and commercially important in Southeast Asian tropical rainforests. For sustainable management of forest ecosystems and conservation of biodiversity, it is essential to establish plantation methods ensuring that genetic variation of the planted trees is equivalent to that in natural forests. The genetic diversity and differentiation of Shorea leprosula and Shorea parvifolia on plantations managed by a private-sector forestry company in Indonesia and those in natural populations were compared using microsatellite markers. Genetic diversity in the planted populations was as high as that in the natural populations. No clear genetic differences between each planted population and the natural forest populations were found. The genetic variation present in planted S. leprosula and S. parvifolia populations did not appear to deteriorate in the planting system implemented in Indonesia, known as Tebang Pilih Tanam Jalur (TPTJ). These results indicate that the current plantation method practiced in the region is suitable for maintaining the original genetic composition and achieving sustainable use of tropical rainforests.

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