Differences in population structure require habitat-specific conservation strategies in the threatened steppe grassland plant Astragalus exscapus

Pinus aristata Engelm., Rocky Mountain bristlecone pine, has a narrow core geographic and elevational distribution, occurs in disjunct populations, and is threatened by rapid climate change, white pine blister rust, and bark beetles. Knowledge of genetic diversity and population structure will help guide gene conservation strategies for this species. Sixteen sites across four mountain ranges in the core distribution of P. aristata were sampled and genetic diversity was assessed with 21 isozyme loci. Low species and population level genetic diversity (He = 0.070 and 0.062, respectively) occurred with moderate among-population differentiation (FST = 0.131). Genetic diversity correlated with longitude, latitude, and elevation and a strong mountain island effect may contribute to substructuring and isolation. Using multiple complementary analyses, sampled trees were assigned to three genetic lineages that varied in diversity and admixture and were associated with different climatic factors. The distribution of genetic diversity and substructuring of P. aristata may be an outcome of a combination of restricted gene flow due to geographic and phenological isolation, random processes of genetic drift, life history traits, natural selection, and postglacial migrations. The combination of low genetic diversity, moderate population isolation, and a protracted regeneration dynamic puts populations at risk for extirpation by novel stresses.

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Coalescence times, life history traits and conservation concerns: an example from four coastal shark species from the Indo-Pacific

10.22541/au.161963333.37636342/v2 ◽

2021 ◽

Author(s):

Pierre Lesturgie ◽

Serge Planes ◽

Stefano Mona

Keyword(s):

Population Structure ◽

Life History ◽

Life History Traits ◽

New Caledonia ◽

Demographic History ◽

Conservation Strategies ◽

Shark Species ◽

Effective Population ◽

Demographic Models ◽

Mobile Species

Dispersal abilities play a crucial role in shaping the extent of population genetic structure, with more mobile species being panmictic over large geographic ranges and less mobile ones organized in meta-populations exchanging migrants to different degrees. In turn, population structure directly influences the coalescence pattern of the sampled lineages, but the consequences on the estimated variation of the effective population size (Ne) over time obtained by means of unstructured demographic models remain poorly understood. However, this knowledge is crucial for biologically interpreting the observed Ne trajectory and further devising conservation strategies in endangered species. Here we investigated the demographic history of four shark species (Carharhinus melanopterus, Carharhinus limbatus, Carharhinus amblyrhynchos, Galeocerdo cuvier) with different degrees of endangered status and life history traits related to dispersal distributed in the Indo-Pacific and sampled off New Caledonia. We compared several evolutionary scenarios representing both structured (meta-population) and unstructured models and then inferred the Ne variation through time. By performing extensive coalescent simulations, we provided a general framework relating the underlying population structure and the observed Ne dynamics. On this basis, we concluded that the recent decline observed in three out of the four considered species when assuming unstructured demographic models can be explained by the presence of population structure. Furthermore, we also demonstrated the limits of the inferences based on the sole site frequency spectrum and warn that statistics based on linkage disequilibrium will be needed to exclude recent demographic events affecting meta-populations.

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The genetic diversity and population structure of two endemic Amazonian quillwort (Isoetes L.) species

PeerJ ◽

10.7717/peerj.10274 ◽

2020 ◽

Vol 8 ◽

pp. e10274 ◽

Cited By ~ 1

Author(s):

Mirella Pupo Santos ◽

João V.S. Rabelo Araujo ◽

Arthur V. Sant’anna Lopes ◽

Julio Cesar Fiorio Vettorazzi ◽

Marcela Santana Bastos Boechat ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Geographical Location ◽

Inter Simple Sequence Repeat ◽

Shannon Index ◽

Conservation Strategies ◽

Amazon Forest ◽

Mass Extinctions ◽

Effective Conservation

Background Two endemic lycophyte species Isoetes cangae and Isoetes serracarajensis have been recently described in the State of Pará in the Amazon forest located in northern Brazil. Isoetes L. has survived through three mass extinctions. Plants are considered small-sized, heterosporous, and can display a great diversity of physiological adaptations to different environments. Thus, the current study aimed to estimate the genetic variation of the populations of I. cangae and I. serracarajensis to generate information about their different mechanisms for survival at the same geographical location that could point to different reproductive, adaptative and dispersal strategies and should be considered for effective conservation strategies. Methods The genetic diversity and population structure of I. cangae and I. serracarajensis were investigated using Inter Simple Sequence Repeat (ISSR) molecular markers. Total genomic DNA was isolated, and the genetic diversity parameters were calculated. Results The sixteen primers produced 115 reproducible bands, 87% of which were polymorphic. A high level of polymorphic loci (81.74% and 68.48%) and a high Shannon index (Sh = 0.376 and 0.289) were observed for I. cangae and I. serracarajensis, respectively. The coefficient of genetic differentiation between population areas (GST) showed a higher value in I. serracarajensis (0.5440). Gene flow was higher in I. cangae (1.715) and lower in I. serracarajensis populations (0.419). Overall, the results further show that I. serracarajensis and I. cangae are two species with considerable genetic variation and that these differences may reflect their habitats and modes of reproduction. These results should be considered in the development of effective conservation strategies for both species.

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Evidence supporting panmixia in Greenland halibut (Reinhardtius hippoglossoides) in the Northwest Atlantic

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/cjfas-2014-0004 ◽

2014 ◽

Vol 71 (5) ◽

pp. 763-774 ◽

Cited By ~ 19

Author(s):

Denis Roy ◽

David C. Hardie ◽

Margaret A. Treble ◽

James D. Reist ◽

Daniel E. Ruzzante

Keyword(s):

Population Structure ◽

Population Genetic ◽

Conservation Strategies ◽

Greenland Halibut ◽

Northwest Atlantic ◽

Population Genetic Differentiation ◽

Conservation Implications ◽

Greenland Halibut Reinhardtius Hippoglossoides ◽

Reinhardtius Hippoglossoides ◽

Species Specific

Assessment of population structure is critical to the design and implementation of sound management and conservation strategies. However, population structure must be assessed using markers attuned to population genetic processes such as genetic drift and gene flow, which reflect actual levels of reproductive isolation among putative genetic clusters. This is critical for highly exploited, commercial species that form the backbone of regional and local economies. Here, we show extremely low levels of population genetic differentiation among Greenland halibut (Reinhardtius hippoglossoides) collected from throughout the Northwest Atlantic, which cannot be statistically differentiated from panmixia using 12 species-specific polymorphic microsatellite markers. In contrast, some previous studies have demonstrated significant differences among individuals collected from various parts of the species’ range using a variety of both genetic and nongenetic techniques. In accordance with other reports and consistent with the species’ life history, we demonstrate that the most parsimonious explanation reconciling observed patterns is a repeated high degree of local differentiation of new recruits and colonizers originating from a common gene pool. Such a scenario has important conservation implications in terms of devising more appropriate strategies balancing species persistence and replenishment with sustainable resource use.

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Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds

Animals ◽

10.3390/ani10081441 ◽

2020 ◽

Vol 10 (8) ◽

pp. 1441

Author(s):

Filippo Cendron ◽

Francesco Perini ◽

Salvatore Mastrangelo ◽

Marco Tolone ◽

Andrea Criscione ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Conservation Status ◽

Geographical Area ◽

Snp Array ◽

Local Economy ◽

Conservation Strategies ◽

Snp Analysis ◽

Runs Of Homozygosity ◽

Chicken Breeds

The genomic variability of local Italian chicken breeds, which were monitored under a conservation plan, was studied using single nucleotide polymorphisms (SNPs) to understand their genetic diversity and population structure. A total of 582 samples from 23 local breeds and four commercial stocks were genotyped using the Affymetrix 600 K Chicken SNP Array. In general, the levels of genetic diversity, investigated through different approaches, were lowest in the local chicken breeds compared to those in the commercial stocks. The level of genomic inbreeding, based on runs of homozygosity (FROH), was markedly different among the breeds and ranged from 0.121 (Valdarnese) to 0.607 (Siciliana). In all breeds, short runs of homozygosity (ROH) (<4 Mb in length) were more frequent than long segments. The patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed non-overlapping clusters and were clearly separate populations, which indicated the presence of gene flow, especially among breeds that originated from the same geographical area. Four genomic regions were identified as hotspots of autozygosity (islands) among the breeds, where the candidate genes are involved in morphological traits, such as body weight and feed conversion ratio. We conclude that the investigated breeds have conserved authentic genetic patterns, and these results can improve conservation strategies; moreover, the conservation of local breeds may play an important role in the local economy as a source of high-quality products for consumers.

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Population structure and partial anadromy in Oncorhynchus mykiss from Kamchatka: relevance for conservation strategies around the Pacific Rim

Ecology Of Freshwater Fish ◽

10.1111/j.1600-0633.2007.00248.x ◽

2007 ◽

Vol 16 (4) ◽

pp. 539-547 ◽

Cited By ~ 55

Author(s):

M. V. McPhee ◽

F. Utter ◽

J. A. Stanford ◽

K. V. Kuzishchin ◽

K. A. Savvaitova ◽

...

Keyword(s):

Population Structure ◽

Oncorhynchus Mykiss ◽

Pacific Rim ◽

Conservation Strategies ◽

The Pacific

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Genetic Diversity and Variability in Endangered Pantesco and Two Other Sicilian Donkey Breeds Assessed by Microsatellite Markers

The Scientific World JOURNAL ◽

10.1100/2012/648427 ◽

2012 ◽

Vol 2012 ◽

pp. 1-6 ◽

Cited By ~ 11

Author(s):

Salvatore Bordonaro ◽

Anna Maria Guastella ◽

Andrea Criscione ◽

Antonio Zuccaro ◽

Donata Marletta

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variability ◽

Genetic Information ◽

Gene Diversity ◽

Genetic Distances ◽

Conservation Strategies ◽

Population Structure Analysis ◽

The Mean ◽

Differentiation Index

The genetic variability of Pantesco and other two Sicilian autochthonous donkey breeds (Ragusano and Grigio Siciliano) was assessed using a set of 14 microsatellites. The main goals were to describe the current differentiation among the breeds and to provide genetic information useful to safeguard the Pantesco breed as well as to manage Ragusano and Grigio Siciliano. In the whole sample, that included 108 donkeys representative of the three populations, a total of 85 alleles were detected. The mean number of alleles was lower in Pantesco (3.7), than in Grigio Siciliano and Ragusano (4.4 and 5.9, resp.). The three breeds showed a quite low level of gene diversity (He) ranging from 0.471 in Pantesco to 0.589 in Grigio. The overall genetic differentiation index (Fst) was quite high; more than 10% of the diversity was found among breeds. Reynolds’ () genetic distances, correspondence, and population structure analysis reproduced the same picture, revealing that, (a) Pantesco breed is the most differentiated in the context of the Sicilian indigenous breeds, (b) within Ragusano breed, two well-defined subgroups were observed. This information is worth of further investigation in order to provide suitable data for conservation strategies.

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Chloroplast microsatellites reveal genetic diversity and population structure in natural populations of Himalayan Cedar (Cedrus deodara (Roxb.) G. Don) in India

Silvae Genetica ◽

10.2478/sg-2020-0012 ◽

2020 ◽

Vol 69 (1) ◽

pp. 86-93

Author(s):

H. S. Ginwal ◽

Rajesh Sharma ◽

Priti Chauhan ◽

Kirti Chamling Rai ◽

Santan Barthwal

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Natural Populations ◽

Conservation Strategies ◽

Restricted Gene Flow ◽

Chloroplast Microsatellites ◽

Timber Species ◽

Western Himalayas ◽

Cedrus Deodara ◽

High Level

AbstractHimalayan cedar (Cedrus deodara) is one of the most important temperate timber species of Western Himalayas and is considered to be among the endangered conifer species in the region. Knowledge of genetic diversity and population structure will help guide gene conservation strategies for this species. Ten polymorphic chloroplast microsatellites (cpSSR) were used to study genetic diversity and population structure in twenty one natural populations of C. deodara throughout its entire distribution range in Western Himalayas. When alleles at each of the 10 loci were jointly analysed, 254 different haplotypes were identified among 1050 individuals. The cpSSRs indicate that C. deodara forests maintain a moderately high level of genetic diversity (mean h = 0.79 ). AMOVA analysis showed that most of the diversity in C. deodara occurs within populations. Bayesian analysis for population structure (BAPS) revealed spatial structuration of the variation (22 % of the total variation) and substructuring captured nineteen genetic clusters in the entire divisions of the populations. Most of the populations were clustered independently with minor admixtures. The distribution of genetic diversity and sub-structuring of C. deodara may be due to restricted gene flow due to geographic isolation, genetic drift, and natural selection. These findings indicated existence of genetically distinct and different high diversity and low diversity clusters, which are potential groups of populations that require attention for their conservation and management. The results are interpreted in context of future conservation plans for C. deodara.

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A Demographic Model of an Endangered Florida Native Bromeliad (Tillandsia utriculata)

Spora A Journal of Biomathematics ◽

10.30707/spora6.1/zuai3621 ◽

2020 ◽

Vol 6 (1) ◽

Author(s):

Zoe Brookover ◽

Alexandra Campbell ◽

Brian Christman ◽

Sydney Davis ◽

Erin Bodine

Keyword(s):

Germination Rate ◽

Model Analysis ◽

Population Viability ◽

Leaf Length ◽

Conservation Strategies ◽

Demographic Model ◽

Population Reduction ◽

Viable Population ◽

Specific Conservation ◽

Myakka River

The large, long-lived, epiphytic bromeliad Tillandsia utriculata is currently listed as state-endangered in Florida due to significant population reduction from predation by an invasive weevil, Metamasius callizona. We have developed a novel demographic model of a population of T. utriculata in Myakka River State Park (MRSP) in Sarasota, Florida using a stage-structured matrix model. Analysis of the model revealed conditions for population viability over a variety of parameter scenarios. Model analysis showed that without weevil predation the minimum germination rate required for population viability is low (4–16%), and that given a viable population at structural equilibrium we would expect to find <1% of the population in flower or post-flowering each year and, at most, about 10% of rosettes with longest leaf length (LLL) > 15 cm in flower or post-flowering each year. Additionally, the model presented here provides a basis for further analyses which explore specific conservation strategies.

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Population structure and adaptive variation of Helichrysum italicum (Roth) G. Don along eastern Adriatic temperature and precipitation gradient

Scientific Reports ◽

10.1038/s41598-021-03548-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Tonka Ninčević ◽

Marija Jug-Dujaković ◽

Martina Grdiša ◽

Zlatko Liber ◽

Filip Varga ◽

...

Keyword(s):

Population Structure ◽

Genetic Variation ◽

Genetic Differentiation ◽

Environmental Gradient ◽

Conservation Strategies ◽

Mediterranean Plants ◽

Outlier Loci ◽

Precipitation Seasonality ◽

Genetic Diversity And Structure ◽

Bioclimatic Variables

AbstractImmortelle (Helichrysum italicum (Roth) G. Don; Asteraceae) is a perennial plant species native to the Mediterranean region, known for many properties with wide application mainly in perfume and cosmetic industry. A total of 18 wild H. italicum populations systematically sampled along the eastern Adriatic environmental gradient were studied using AFLP markers to determine genetic diversity and structure and to identify loci potentially responsible for adaptive divergence. Results showed higher levels of intrapopulation diversity than interpopulation diversity. Genetic differentiation among populations was significant but low, indicating extensive gene flow between populations. Bayesian analysis of population structure revealed the existence of two genetic clusters. Combining the results of FST - outlier analysis (Mcheza and BayeScan) and genome-environment association analysis (Samβada, LFMM) four AFLP loci strongly associated with the bioclimatic variables Bio03 Isothermality, Bio08 Mean temperature of the wettest quarter, Bio15 Precipitation seasonality, and Bio17 Precipitation of driest quarter were found to be the main variables driving potential adaptive genetic variation in H. italicum along the eastern Adriatic environmental gradient. Redundancy analysis revealed that the partitioning of genetic variation was mainly associated with the adaptation to temperature oscillations. The results of the research may contribute to a clearer understanding of the importance of local adaptations for the genetic differentiation of Mediterranean plants and allow the planning of appropriate conservation strategies. However, considering that the identified outlier loci may be linked to genes under selection rather than being the target of natural selection, future studies must aim at their additional analysis.

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