Landscape genetics in mammals

AbstractThe focus of this review is on landscape genetics (LG), a relatively new discipline that arose approximately 10 years ago. LG spans the interface between population genetics and landscape ecology and thus incorporates the concepts, methods, and tools from both disciplines. On the basis of an understanding of the spatial distribution of genetic diversity, LG aims to explain how landscape and environmental characteristics influence microevolutionary processes and metapopulation dynamics, including gene flow (i.e., connectivity) and selection (i.e., local adaptations). LG is concerned with events that occurred during the recent time scale, and the individual is the operational unit. As a discipline that combines spatial genetic diversity with ecological features, LG is able to address questions relating to different evolutionary processes. We illustrate some of these here using examples taken from mammals: population structure; gene flow and the identification of barriers; fragmentation, connectivity, and corridors; local adaptation and selection; there are two different questions: applications in conservation genetics; and future developments in LG. We will then present the methods and tools commonly used in the different steps of LG analyses: the genetic and landscape sampling, the quantification of genetic variation, the characterization of spatial landscape structures, and finally, the correlation between genetic patterns and landscape features.

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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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Genetic diversity of local cattle*

Acta Biochimica Polonica ◽

10.18388/abp.2017_2347 ◽

2018 ◽

Vol 65 (3) ◽

Cited By ~ 2

Author(s):

Veronika Kukučková ◽

Nina Moravčíková ◽

Ino Curik ◽

Mojca Simčič ◽

Gábor Mészáros ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Population Size ◽

Clustering Algorithm ◽

Marginal Likelihood ◽

Population Decline ◽

Bottleneck Effect ◽

High Gene ◽

Historical Origin

The Slovak Pinzgau breed faces the bottleneck effect and the loss of diversity due to unequal use of founders and significant population decline. Further population size reduction can lead to serious problems. High-throughput genotypes of 179 individuals were used to characterise genetic diversity and differentiation of Slovak Pinzgau, Austrian Pinzgau, Cika and Piedmontese cattle by Bayesian clustering algorithm. A gene flow network for the clusters estimated from admixture results was produced. The low estimate of genetic differentiation (FST) in Pinzgau cattle populations indicated that differentiation among these populations is low, particularly owing to a common historical origin and high gene flow. The changes in the log marginal likelihood indicated Austrian Pinzgau as the most similar breed to Slovak Pinzgau. All populations except Piedmontese showed two ways of gene flow among populations indicating that Piedmontese was involved in formation of analysed breeds while these breeds were not involved in creation of Piedmontese. Genetic evaluation represents an important tool in breeding and cattle selection. It is more strategically important than ever to preserve as much of the livestock diversity as possible, to ensure a prompt and proper response to the needs of future generations. The information provided by the fine-scale genetic characterization of this study clearly shows that there is a difference in genetic composition of Slovak and Austrian populations as well as Cika and Piedmontese. Slovak Pinzgau cattle despite its population size has the potential to serve as a basic gene reserve of this breed with the European and World importance.

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Molecular Characterization of Lates niloticus (Perciformes, Latidae) Populations from three Nigerian Waterbodies using Random Amplified Polymorphic DNA and Microsatellite Markers

Vestnik Zoologii ◽

10.1515/vzoo-2017-0005 ◽

2017 ◽

Vol 51 (1) ◽

pp. 31-36

Author(s):

K. E. Ogbuebunu ◽

M. O. Awodiran

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Gene Flow ◽

Microsatellite Markers ◽

Random Amplified Polymorphic Dna ◽

Population Level ◽

Effective Number ◽

Lates Niloticus ◽

The Mean

Abstract Thirty Lates niloticus (Linnaeus, 1758) from three Nigerian waterbodies were genotyped on six RAPD primers and five microsatellites loci. RAPD revealed that effective number of alleles (AE) at population level per locus was within the range of 1.641 ± 0.066 to 1.645 ± 0.041 while the mean number of alleles (AN) across populations equals 2.000. Characterization on five microsatellites loci revealed genetic diversity within and among studied populations. Observed heterozygousity (HO) was within the range of 0.317 ± 0.335 to 0.523 ± 0.315 while expected heterozygousity (HE) was within the range of 0.414 ± 0.306 to 0.715 ± 0.097. Proportion of differentiation (FST) within populations was 0.236. Overall gene flow (Nm) among populations equals 0.806. This study established the successful use of RAPD and microsatellite as tools for studying population structure of fish species, especially L. niloticus. Thus, it can be concluded that L. niloticus in the three (3) sampled Nigerian waterbodies is undergoing evolution.

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Global wind patterns shape genetic differentiation, asymmetric gene flow, and genetic diversity in trees

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2017317118 ◽

2021 ◽

Vol 118 (17) ◽

pp. e2017317118

Author(s):

Matthew M. Kling ◽

David D. Ackerly

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Large Scale ◽

Landscape Connectivity ◽

Genetic Data ◽

Plant Ecology ◽

Wind Pollination ◽

Genetic Patterns ◽

Partial Correlations ◽

Wind Currents

Wind disperses the pollen and seeds of many plants, but little is known about whether and how it shapes large-scale landscape genetic patterns. We address this question by a synthesis and reanalysis of genetic data from more than 1,900 populations of 97 tree and shrub species around the world, using a newly developed framework for modeling long-term landscape connectivity by wind currents. We show that wind shapes three independent aspects of landscape genetics in plants with wind pollination or seed dispersal: populations linked by stronger winds are more genetically similar, populations linked by directionally imbalanced winds exhibit asymmetric gene flow ratios, and downwind populations have higher genetic diversity. For each of these distinct hypotheses, partial correlations between the respective wind and genetic metrics (controlling for distance and climate) are positive for a significant majority of wind-dispersed or wind-pollinated genetic data sets and increase significantly across functional groups expected to be increasingly influenced by wind. Together, these results indicate that the geography of both wind strength and wind direction play important roles in shaping large-scale genetic patterns across the world’s forests. These findings have implications for various aspects of basic plant ecology and evolution, as well as the response of biodiversity to future global change.

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Genetic rescue by augmenting gene flow

10.1093/oso/9780198783398.003.0006 ◽

2017 ◽

Author(s):

Richard Frankham ◽

Jonathan D. Ballou ◽

Katherine Ralls ◽

Mark D. B. Eldridge ◽

Michele R. Dudash ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Inbreeding Coefficient ◽

Outbreeding Depression ◽

Genetic Rescue ◽

Evolutionary Potential ◽

Beneficial Effects ◽

The Difference ◽

Inbred Populations ◽

Harmful Effects

Inbreeding is reduced and genetic diversity enhanced when a small isolated inbred population is crossed to another unrelated population. Crossing can have beneficial or harmful effects on fitness, but beneficial effects predominate, and the risks of harmful ones (outbreeding depression) can be predicted and avoided. For crosses with a low risk of outbreeding depression, there are large and consistent benefits on fitness that persist across generations in outbreeding species. Benefits are greater in species that naturally outbreed than those that inbreed, and increase with the difference in inbreeding coefficient between crossed and inbred populations in mothers and zygotes. However, benefits are similar across invertebrates, vertebrates and plants. There are also important benefits for evolutionary potential of crossing between populations.

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Mitogenomics of the endangered Mediterranean monk seal (Monachus monachus) reveals dramatic loss of diversity and supports historical gene-flow between Atlantic and eastern Mediterranean populations

Zoological Journal of the Linnean Society ◽

10.1093/zoolinnean/zlaa084 ◽

2020 ◽

Author(s):

Alba Rey-Iglesia ◽

Philippe Gaubert ◽

Gonçalo Espregueira Themudo ◽

Rosa Pires ◽

Constanza De La Fuente ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

North Atlantic ◽

Marine Mammals ◽

Eastern Mediterranean ◽

The Black Sea ◽

Mediterranean Populations ◽

Geographic Ranges ◽

Western Sahara ◽

The Mediterranean

Abstract The Mediterranean monk seal Monachus monachus is one of the most threatened marine mammals, with only 600–700 individuals restricted to three populations off the coast of Western Sahara and Madeira (North Atlantic) and between Greece and Turkey (eastern Mediterranean). Its original range was from the Black Sea (eastern Mediterranean) to Gambia (western African coast), but was drastically reduced by commercial hunting and human persecution since the early stages of marine exploitation. We here analyse 42 mitogenomes of Mediterranean monk seals, from across their present and historical geographic ranges to assess the species population dynamics over time. Our data show a decrease in genetic diversity in the last 200 years. Extant individuals presented an almost four-fold reduction in genetic diversity when compared to historical specimens. We also detect, for the first time, a clear segregation between the two North Atlantic populations, Madeira and Cabo Blanco, regardless of their geographical proximity. Moreover, we show the presence of historical gene-flow between the two water basins, the Atlantic Ocean and the Mediterranean Sea, and the presence of at least one extinct maternal lineage in the Mediterranean. Our work demonstrates the advantages of using full mitogenomes in phylogeographic and conservation genomic studies of threatened species.

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Separation and Characterization of Standard Propoxyphene Diastereomers and Their Determination in Pharmaceutical and Illicit Preparations

Journal of AOAC INTERNATIONAL ◽

10.1093/jaoac/64.4.875 ◽

1981 ◽

Vol 64 (4) ◽

pp. 875-883

Author(s):

Shiv K Soni ◽

Daniel Van Gelder

Keyword(s):

High Pressure ◽

Optical Isomers ◽

Gold Chloride ◽

Melting Points ◽

Eutectic Melting ◽

Racemic Mixtures ◽

The Individual ◽

Isomeric Mixtures ◽

Asymmetric Carbon

Abstract Due to the existence of 2 asymmetric carbon atoms in: the propoxyphene molecule, there are 4 diastereomers: alpha dextro, alpha levo, beta dextro, and beta levo. Only α-d-propoxyphene is included under the federal Controlled Substances Act. Baseline separations of propoxyphene from various incipients (aspirin, caffeine, phenacetin, and acetaminophen) present in pharmaceutical and illicit preparations, and between the alpha and beta diastereomers, were achieved by high pressure liquid chromatography. The column eluant was collected and propoxyphene was extracted. The optical isomers were differentiated and characterized by melting points and by chemical microcrystalline tests. Using hot stage thermomicroscopy, the eutectic melting points of binary isomeric mixtures of propoxyphene bases and salts were found to be depressed about 10° and 15-30°C, respectively, below the individual isomer melting points. The characteristic microcrystals formed with the alpha racemic mixtures by using a glycerin-aqueous gold chloride reagent were not produced by the beta racemic mixtures.

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Influence of environmental factors on the genetic variation of the aquatic macrophyte Ranunculus subrigidus on the Qinghai-Tibetan Plateau

BMC Evolutionary Biology ◽

10.1186/s12862-019-1559-0 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 2

Author(s):

Zhigang Wu ◽

Xinwei Xu ◽

Juan Zhang ◽

Gerhard Wiegleb ◽

Hongwei Hou

Keyword(s):

Genetic Diversity ◽

Tibetan Plateau ◽

Environmental Factors ◽

Local Adaptation ◽

Aquatic Macrophyte ◽

Spatial Genetic Structure ◽

Long Distance ◽

Elevation Gradients ◽

Mantel Tests ◽

Genetic Patterns

Abstract Background Due to the environmental heterogeneity along elevation gradients, alpine ecosystems are ideal study objects for investigating how ecological variables shape the genetic patterns of natural species. The highest region in the world, the Qinghai-Tibetan Plateau, is a hotspot for the studies of evolutionary processes in plants. Many large rivers spring from the plateau, providing abundant habitats for aquatic and amphibious organisms. In the present study, we examined the genetic diversity of 13 Ranunculus subrigidus populations distributed throughout the plateau in order to elucidate the relative contribution of geographic distance and environmental dissimilarity to the spatial genetic pattern. Results A relatively low level of genetic diversity within populations was found. No spatial genetic structure was suggested by the analyses of molecular variance, Bayesian clustering analysis and Mantel tests. Partial Mantel tests and multiple matrix regression analysis showed a significant influence of the environment on the genetic divergence of the species. Both climatic and water quality variables contribute to the habitat heterogeneity of R. subrigidus populations. Conclusions Our results suggest that historical processes involving long-distance dispersal and local adaptation may account for the genetic patterns of R. subrigidus and current environmental factors play an important role in the genetic differentiation and local adaptation of aquatic plants in alpine landscapes.

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