Applied phylogeography of Cyclopia intermedia (Fabaceae) highlights the need for ‘duty of care’ when cultivating honeybush

Background The current cultivation and plant breeding of Honeybush tea (produced from members of CyclopiaVent.) do not consider the genetic diversity nor structuring of wild populations. Thus, wild populations may be at risk of genetic contamination if cultivated plants are grown in the same landscape. Here, we investigate the spatial distribution of genetic diversity within Cyclopia intermedia E. Mey.—this species is widespread and endemic in the Cape Floristic Region (CFR) and used in the production of Honeybush tea. Methods We applied High Resolution Melt analysis (HRM), with confirmation Sanger sequencing, to screen two non-coding chloroplast DNA regions (two fragments from the atpI-aptH intergenic spacer and one from the ndhA intron) in wild C. intermedia populations. A total of 156 individuals from 17 populations were analyzed for phylogeographic structuring. Statistical tests included analyses of molecular variance and isolation-by-distance, while relationships among haplotypes were ascertained using a statistical parsimony network. Results Populations were found to exhibit high levels of genetic structuring, with 62.8% of genetic variation partitioned within mountain ranges. An additional 9% of genetic variation was located amongst populations within mountains, suggesting limited seed exchange among neighboring populations. Despite this phylogeographic structuring, no isolation-by-distance was detected (p > 0.05) as nucleotide variation among haplotypes did not increase linearly with geographic distance; this is not surprising given that the configuration of mountain ranges dictates available habitats and, we assume, seed dispersal kernels. Conclusions Our findings support concerns that the unmonitored redistribution of Cyclopia genetic material may pose a threat to the genetic diversity of wild populations, and ultimately the genetic resources within the species. We argue that ‘duty of care’ principles be used when cultivating Honeybush and that seed should not be translocated outside of the mountain range of origin. Secondarily, given the genetic uniqueness of wild populations, cultivated populations should occur at distance from wild populations that is sufficient to prevent unintended gene flow; however, further research is needed to assess gene flow within mountain ranges.

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Elucidating the drivers of genetic differentiation in Malaysian torrent frogs (Anura: Ranidae: Amolops): a landscape genomics approach

Zoological Journal of the Linnean Society ◽

10.1093/zoolinnean/zlz151 ◽

2019 ◽

Vol 190 (1) ◽

pp. 65-78 ◽

Cited By ~ 2

Author(s):

Kin Onn Chan ◽

Rafe M Brown

Keyword(s):

Genetic Variation ◽

Gene Flow ◽

Genetic Differentiation ◽

Isolation By Distance ◽

Variance Partitioning ◽

Nucleotide Polymorphisms ◽

Landscape Genomics ◽

Mountain Ranges ◽

Historical Factors ◽

Environmental Attributes

Abstract The interplay between environmental attributes and evolutionary processes can provide valuable insights into how biodiversity is generated, partitioned and distributed. This study investigates the role of spatial, environmental and historical factors that could potentially drive diversification and shape genetic variation in Malaysian torrent frogs. Torrent frogs are ecologically conserved, and we hypothesize that this could impose tight constraints on dispersal routes, gene flow and consequently genetic structure. Moreover, levels of gene flow were shown to vary among populations from separate mountain ranges, indicating that genetic differentiation could be influenced by landscape features. Using genome-wide single nucleotide polymorphisms, in conjunction with landscape variables derived from Geographic Information Systems, we performed distance-based redundancy analyses and variance partitioning to disentangle the effects of isolation-by-distance (IBD), isolation-by-resistance (IBR) and isolation-by-colonization (IBC). Our results demonstrated that IBR contributed minimally to genetic variation. Intraspecific population structure can be largely attributed to IBD, whereas interspecific diversification was primarily driven by IBC. We also detected two distinct population bottlenecks, indicating that speciation events were likely driven by vicariance or founder events.

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Regional and Population-scale Influences on Genetic Diversity Partitioning within Costa Rican Populations of the Pioneer Tree Vochysia ferruginea Mart

Silvae Genetica ◽

10.1515/sg-2005-0037 ◽

2005 ◽

Vol 54 (1-6) ◽

pp. 258-264 ◽

Cited By ~ 12

Author(s):

S. Cavers ◽

C. Navarro ◽

P. Hopkins ◽

R. A. Ennos ◽

A. J. Lowe

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Isolation By Distance ◽

Costa Rican ◽

Population Diversity ◽

Mountain Range ◽

Pioneer Species ◽

Contemporary Gene Flow ◽

Sustainable Utilisation ◽

Vochysia Ferruginea

Abstract The neotropical pioneer species Vochysia ferruginea is locally important for timber and is being increasingly exploited. The sustainable utilisation of this species would benefit from an understanding of the level and partitioning of genetic diversity within remnant and secondary regrowth populations. We used data from total genome (amplified fragment length polymorphism, AFLP) and chloroplast genome markers to assay diversity levels within seven Costa Rican populations. Significant chloroplast differentiation between Atlantic and Pacific watersheds was observed, suggesting divergent historical origins for these populations. Contemporary gene flow, though extensive, is geographically constrained and a clear pattern of isolation by distance was detectable when an inter-population distance representing gene flow around the central Costa Rican mountain range was used. Overall population differentiation was low (FST = 0.15) and within-population diversity high, though variable (Hs = 0.16-0.32), which fits with the overall pattern of population genetic structure expected for a widespread, outcrossed tropical tree. However genetic diversity was significantly lower and differentiation higher for recently colonised and disturbed populations compared to that at more established sites. Such a pattern seems indicative of a pioneer species undergoing repeated cycles of colonisation and succession.

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Linking patterns of genetic variation to processes of diversification in Malaysian torrent frogs (Anura: Ranidae:Amolops): a landscape genomics approach

10.1101/628891 ◽

2019 ◽

Cited By ~ 2

Author(s):

Kin Onn Chan ◽

Rafe M. Brown

Keyword(s):

Genetic Variation ◽

Gene Flow ◽

Isolation By Distance ◽

Variance Partitioning ◽

Population Bottlenecks ◽

Landscape Genomics ◽

Mountain Ranges ◽

Historical Factors ◽

Environmental Attributes ◽

Isolation By Environment

ABSTRACTThe interplay between environmental attributes and evolutionary processes can provide valuable insights into how biodiversity is generated, partitioned, and distributed. This study investigates the role of spatial, environmental, and historical factors that could potentially drive diversification and shape genetic variation in Malaysian torrent frogs. Torrent frogs are ecologically conserved, and we hypothesize that this could impose tight constraints on dispersal routes, gene flow, and consequently genetic structure. Moreover, levels of gene flow were shown to vary among populations from separate mountain ranges, indicating that genetic differentiation could be influenced by landscape features. Using genome-wide SNPs in conjunction with landscape variables derived from GIS, we performed distance-based redundancy analyses and variance partitioning to disentangle the effects of isolation-by-distance (IBD), isolation-by-environment (IBE), and isolation-by-colonization (IBC). Our results demonstrated that IBE, contributed minimally to genetic variation. Intraspecific population structure can be largely attributed to IBD, whereas interspecific diversification was primarily driven by IBC. We also detected two distinct population bottlenecks, indicating that speciation events were likely driven by vicariance or founder events.

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Genetic melting pot and importance of long-distance dispersal indicated in the Gladiolus imbricatus L. populations in the Polish Carpathians

Scientific Reports ◽

10.1038/s41598-021-96135-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Agnieszka Sutkowska ◽

Józef Mitka ◽

Tomasz Warzecha ◽

Jakub Bunk ◽

Julia Rutkowska ◽

...

Keyword(s):

Genetic Diversity ◽

Diversity Indices ◽

Western Carpathians ◽

Genetic Structuring ◽

Long Distance ◽

Plant Populations ◽

Genetic Stock ◽

Melting Pot ◽

Mountain Ranges ◽

Eastern Carpathians

AbstractThe genetic diversity in 11 populations of Gladiolus imbricatus in five mountain ranges, including the Tatra, Pieniny, Gorce, Beskid Niski (Western Carpathians) and Bieszczady Mts (Eastern Carpathians), was studied with inter-simple sequence repeat (ISSR) markers. The species is a perennial plant occurring in open and semi-open sites of anthropogenic origin (meadows and forest margins). We checked a hypothesis on the microrefugial character of the plant populations in the Pieniny Mts, a small calcareous Carpathian range of complicated relief that has never been glaciated. Plant populations in the Tatra and Pieniny Mts had the highest genetic diversity indices, pointing to their long-term persistence. The refugial vs. the non-refugial mountain ranges accounted for a relatively high value of total genetic variation [analysis of molecular variance (AMOVA), 14.12%, p = 0.003]. One of the Pieniny populations was of hybridogenous origin and shared genetic stock with the Tatra population, indicating there is a local genetic melting pot. A weak genetic structuring of populations among particular regions was found (AMOVA, 4.5%, p > 0.05). This could be an effect of the frequent short-distance and sporadic long-distance gene flow. The dispersal of diaspores between the remote populations in the Western Carpathians and Eastern Carpathians could be affected by the historical transportation of flocks of sheep from the Tatra to Bieszczady Mts.

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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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Population genetic structure and variability in Lindera glauca (Lauraceae) indicates low levels of genetic diversity and skewed sex ratios in natural populations in mainland China

PeerJ ◽

10.7717/peerj.8304 ◽

2020 ◽

Vol 8 ◽

pp. e8304 ◽

Cited By ~ 2

Author(s):

Biao Xiong ◽

Limei Zhang ◽

Shubin Dong ◽

Zhixiang Zhang

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Isolation By Distance ◽

Sex Ratios ◽

Mainland China ◽

Small Sample ◽

Chloroplast Microsatellites ◽

Wild Populations ◽

Haplotype Networks ◽

Low Levels

Lindera glauca (Lauraceae) is a tree of economic and ecological significance that reproduces sexually and asexually via apomictic seeds. It is widely distributed in the low-altitude montane forests of East Asia. Despite the potential implications of a mixed reproductive system in terms of genetic diversity, few studies have focused on this aspect. In this study, the genetic structure of wild populations of L. glauca was investigated via genetic analyses. Overall, 13 nuclear microsatellites (nSSRs) and five chloroplast microsatellites (cpSSRs) were used to genotype 300 individual plants, taken from 20 wild populations (a small sample size in some wild populations is due to the limitation of its specific reproduction, leading to certain limitations in the results of this study) and two cultivated populations ranging across nearly the entire natural distribution of mainland China. The populations exhibited low levels of genetic diversity (nSSR: AR = 1.75, Ho = 0.32, He = 0.36; cpSSR: Nb = 2.01, Hrs = 0.40), and no significant effect of isolation by distance between populations existed, regardless of marker type (nSSR: R2 = 0.0401, P = 0.068; cpSSR: R2 = 0.033, P = 0.091). Haplotype networks showed complex relationships among populations, and the H12 haplotype was predominant in most populations. Analyses of molecular variance obtained with nuclear markers (Fsc = 0.293, FST = 0.362) and chloroplast markers (Fsc = 0.299, FST = 0.312) were similar. The migration ratio of pollen flow versus seed flow in this study was negative (r = −1.149). Results suggest that weak barriers of dispersal between populations and/or the similarity of founders shared between neighbors and distant populations are indicative of the gene flow between populations more likely involving seeds. Wild L. glauca in mainland China was inferred to have highly skewed sex ratios with predominant females. In addition, some populations experienced a recent bottleneck effect, especially in Gujianshan, Chongqing, and southwest China (population GJS). It is suggested that few wild male individuals should be conserved in order to maintain overall genetic diversity in the wild populations of this species. These findings provide important information for the sustainable utilization and preservation of the overall genetic diversity of L. glauca.

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Targeted Sequencing Suggests Wild-Crop Gene Flow Is Central to Different Genetic Consequences of Two Independent Pumpkin Domestications

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2021.618380 ◽

2021 ◽

Vol 9 ◽

Author(s):

Heather R. Kates ◽

Fernando López Anido ◽

Guillermo Sánchez-de la Vega ◽

Luis E. Eguiarte ◽

Pamela S. Soltis ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Gene Flow ◽

Genetic Structure ◽

Morphological Diversity ◽

Cucurbita Maxima ◽

Wild Progenitor ◽

Breeding Potential ◽

Trait Improvement ◽

Wild Progenitors

Studies of domestication genetics enrich our understanding of how domestication shapes genetic and morphological diversity. We characterized patterns of genetic variation in two independently domesticated pumpkins and their wild progenitors to assess and compare genetic consequences of domestication. To compare genetic diversity pre- and post-domestication and to identify genes targeted by selection during domestication, we analyzed ∼15,000 SNPs of 48 unrelated accessions, including wild, landrace, and improved lines for each of two pumpkin species, Cucurbita argyrosperma and Cucurbita maxima. Genetic diversity relative to its wild progenitor was reduced in only one domesticated subspecies, C. argyrosperma ssp. argyrosperma. The two species have different patterns of genetic structure across domestication status. Only 1.5% of the domestication features identified for both species were shared between species. These findings suggest that ancestral genetic diversity, wild-crop gene flow, and domestication practices shaped the genetic diversity of two similar Cucurbita crops in different ways, adding to our understanding of how genetic diversity changes during the processes of domestication and how trait improvement impacts the breeding potential of modern crops.

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Range reduction of the Oblong Rocksnail, Leptoxis compacta, shapes riverscape genetic patterns

10.1101/2020.05.12.090662 ◽

2020 ◽

Author(s):

Aaliyah D. Wright ◽

Nicole L. Garrison ◽

Ashantye’ S. Williams ◽

Paul D. Johnson ◽

Nathan V. Whelan

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Human Impacts ◽

Isolation By Distance ◽

Extinction Risk ◽

River System ◽

High Genetic Diversity ◽

Range Contraction ◽

Genetic Patterns ◽

Cahaba River

AbstractMany freshwater gastropod species face extinction, including 79% of species in the family Pleuroceridae. The Oblong Rocksnail, Leptoxis compacta, is a narrow range endemic pleurocerid from the Cahaba River basin in central Alabama that has seen rapid range contraction in the last 100 years. Such a decline is expected to negatively affect genetic diversity in the species. However, precise patterns of genetic variation and gene flow across the restricted range of L. compacta are unknown. This lack of information limits our understanding of human impacts on the Cahaba River system and Pleuroceridae. Here, we show that L. compacta has likely seen a species-wide decline in genetic diversity, but remaining populations have relatively high genetic diversity. We also report a contemporary range extension compared to the last published survey. Leptoxis compacta does not display an isolation by distance pattern, contrasting patterns seen in many riverine taxa. Our findings also indicate that historical range contraction has resulted in the absence of common genetic patterns seen in many riverine taxa like isolation by distance as the small distribution of L. compacta allows for relatively unrestricted gene flow across its remaining range despite limited dispersal abilities. Two collection sites had higher genetic diversity than others, and broodstock sites for future captive propagation and reintroduction efforts should utilize sites identified here as having the highest genetic diversity. Broadly, our results support the hypothesis that range contraction will result in the reduction of species-wide genetic diversity, and common riverscape genetic patterns cannot be assumed to be present in species facing extinction risk.

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Range reduction of Oblong Rocksnail, Leptoxis compacta, shapes riverscape genetic patterns

PeerJ ◽

10.7717/peerj.9789 ◽

2020 ◽

Vol 8 ◽

pp. e9789

Author(s):

Aaliyah D. Wright ◽

Nicole L. Garrison ◽

Ashantye’ S. Williams ◽

Paul D. Johnson ◽

Nathan V. Whelan

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Human Impacts ◽

Isolation By Distance ◽

Extinction Risk ◽

River System ◽

High Genetic Diversity ◽

Range Contraction ◽

Genetic Patterns ◽

Cahaba River

Many freshwater gastropod species face extinction, including 79% of species in the family Pleuroceridae. The Oblong Rocksnail, Leptoxis compacta, is a narrow range endemic pleurocerid from the Cahaba River basin in central Alabama that has seen rapid range contraction in the last 100 years. Such a decline is expected to negatively affect genetic diversity in the species. However, precise patterns of genetic variation and gene flow across the restricted range of L. compacta are unknown. This lack of information limits our understanding of human impacts on the Cahaba River system and Pleuroceridae. Here, we show that L. compacta has likely seen a species-wide decline in genetic diversity, but remaining populations have relatively high genetic diversity. We also report a contemporary range extension compared to the last published survey. Our findings indicate that historical range contraction has resulted in the absence of common genetic patterns seen in many riverine taxa like isolation by distance as the small distribution of L. compacta allows for relatively unrestricted gene flow across its remaining range despite limited dispersal abilities. Two collection sites had higher genetic diversity than others, and broodstock sites for future captive propagation and reintroduction efforts should utilize sites identified here as having the highest genetic diversity. Broadly, our results support the hypothesis that range contraction will result in the reduction of species-wide genetic diversity, and common riverscape genetic patterns cannot be assumed to be present in species facing extinction risk.

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Weak genetic structuring suggests historically high genetic connectivity among recently fragmented urban populations of the scincid lizard, Ctenotus fallens

Australian Journal of Zoology ◽

10.1071/zo15022 ◽

2015 ◽

Vol 63 (4) ◽

pp. 279 ◽

Cited By ~ 5

Author(s):

Josef Krawiec ◽

Siegfried L. Krauss ◽

Robert A. Davis ◽

Peter B. S. Spencer

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Large Population ◽

Geographic Distance ◽

Genetic Erosion ◽

Genetic Connectivity ◽

Genetic Structuring ◽

Low Genetic Diversity ◽

Population Sizes

Populations in fragmented urban remnants may be at risk of genetic erosion as a result of reduced gene flow and elevated levels of inbreeding. This may have serious genetic implications for the long-term viability of remnant populations, in addition to the more immediate pressures caused by urbanisation. The population genetic structure of the generalist skink Ctenotus fallens was examined using nine microsatellite markers within and among natural vegetation remnants within a highly fragmented urban matrix in the Perth metropolitan area in Western Australia. These data were compared with samples from a large unfragmented site on the edge of the urban area. Overall, estimates of genetic diversity and inbreeding within all populations were similar and low. Weak genetic differentiation, and a significant association between geographic and genetic distance, suggests historically strong genetic connectivity that decreases with geographic distance. Due to recent fragmentation, and genetic inertia associated with low genetic diversity and large population sizes, it is not possible from these data to infer current genetic connectivity levels. However, the historically high levels of gene flow that our data suggest indicate that a reduction in contemporary connectivity due to fragmentation in C. fallens is likely to result in negative genetic consequences in the longer term.

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