scholarly journals The DNA of coral reef biodiversity: predicting and protecting genetic diversity of reef assemblages

2016 ◽  
Vol 283 (1829) ◽  
pp. 20160354 ◽  
Author(s):  
Kimberly A. Selkoe ◽  
Oscar E. Gaggiotti ◽  
Eric A. Treml ◽  
Johanna L. K. Wren ◽  
Mary K. Donovan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Species Interactions ◽  
Allelic Richness ◽  
Coral Cover ◽  
Species Turnover ◽  
Depth Range ◽  
Ecological Communities ◽  
Effective Population ◽  
A Site ◽  
New Strategies

Conservation of ecological communities requires deepening our understanding of genetic diversity patterns and drivers at community-wide scales. Here, we use seascape genetic analysis of a diversity metric, allelic richness (AR), for 47 reef species sampled across 13 Hawaiian Islands to empirically demonstrate that large reefs high in coral cover harbour the greatest genetic diversity on average. We found that a species's life history (e.g. depth range and herbivory) mediates response of genetic diversity to seascape drivers in logical ways. Furthermore, a metric of combined multi-species AR showed strong coupling to species richness and habitat area, quality and stability that few species showed individually. We hypothesize that macro-ecological forces and species interactions, by mediating species turnover and occupancy (and thus a site's mean effective population size), influence the aggregate genetic diversity of a site, potentially allowing it to behave as an apparent emergent trait that is shaped by the dominant seascape drivers. The results highlight inherent feedbacks between ecology and genetics, raise concern that genetic resilience of entire reef communities is compromised by factors that reduce coral cover or available habitat, including thermal stress, and provide a foundation for new strategies for monitoring and preserving biodiversity of entire reef ecosystems.

Species traits influence the genetic consequences of river fragmentation on two co-occurring redhorse (Moxostoma) species

2008 ◽  
Vol 65 (9) ◽  
pp. 1892-1904 ◽  
Author(s):  
Scott M. Reid ◽  
Chris C. Wilson ◽  
Leon M. Carl ◽  
Troy G. Zorn
Keyword(s):  
Genetic Diversity ◽  
Allelic Richness ◽  
Species Traits ◽  
Population Bottlenecks ◽  
Effective Population ◽  
Length Effect ◽  
Microsatellite Dna Markers ◽  
Population Sizes ◽  
River Fragmentation ◽  
Movement Differences

We used microsatellite DNA markers to test whether fragmentation of the Trent River (Ontario, Canada) has reduced genetic diversity and increased genetic differentiation among populations of river redhorse ( Moxostoma carinatum ) and shorthead redhorse (Moxostoma macrolepidotum). Allelic richness of both species was significantly greater along the free-flowing Muskegon River (Michigan, USA) than along the fragmented Trent River. Contrary to expectations, there was no evidence of a fragment length effect on genetic diversity, recent population bottlenecks, or increased relatedness among individuals in fragmented populations. High levels of linkage disequilibrium indicate extinction–recolonization population dynamics along the Trent River. For both species, pairwise FST tests identified weak but statistically significant population differentiation. In the Trent River, differentiation was significantly greater for river redhorse than for shorthead redhorse and, for both species, greater than in the Muskegon River. Moderate fragmentation effects likely reflect the permeability of the dam-lock system to redhorse movement. Differences between species indicate that as a result of smaller effective population sizes, habitat specialists and species at the periphery of their geographic range are more sensitive to river fragmentation.

scholarly journals How many of them? Genetic diversity, survival and effective population size of the capercaillie population from the Gorce Mountains

2019 ◽  
Vol 62 (2) ◽  
pp. 135-144
Author(s):  
Sebastian SZCZEPAŃSKI ◽  
◽  
Anna SANTOREK ◽  
Beata DULISZ ◽  
Zbigniew ŻUREK ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Allelic Richness ◽  
Isolated Population ◽  
Effective Population ◽  
Field Surveys ◽  
Genetic Profiling ◽  
Factors Affecting ◽  
Non Invasive

Population size and effective population size are important factors affecting probability of extinction of small, isolated population. Hence, from conservation perspective, it is recommended to monitor changes in population size of endangered species. Genetic methods, based on genetic profiling of non-invasive samples of biological material, despite some limitations, were proved to be efficient method in tracking individuals in the field and estimate populations' parameters. We used this strategy to investigate isolated population of the capercaillie (Tetrao urogallus) in the Gorce Mountains. In two study periods (2012–2013 and 2017–2018) almost 400 faeces and feathers were collected. Microsatellite genotyping was performed to identify individuals and estimate genetic diversity. We found that population is stable in terms of size and genetic indices, although allelic richness has significantly increased between 2012–2013 and 2017–2018. In the overall study period (2012–2018) there were 52 individuals identified. However, only 10 birds were found in both study periods. This suggests low survival in the population. Moreover, genetic data indicated low effective population size of the capercaillie in the Gorce Mts. Thus, we suggest that monitoring, either genetic and based on field-surveys, should be implemented in the management and protection of this population.

Evolutionary genetics of small populations

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.

Seagrass depth range and water quality in southern Moreton Bay, Queensland, Australia

1996 ◽  
Vol 47 (6) ◽  
pp. 763 ◽  
Author(s):  
EG Abal ◽  
WC Dennison
Keyword(s):  
Water Quality ◽  
Chlorophyll A ◽  
Suspended Solids ◽  
Light Attenuation ◽  
River Mouth ◽  
Total Suspended Solids ◽  
Quality Parameters ◽  
Depth Range ◽  
Moreton Bay ◽  
A Site

Correlations between water quality parameters and seagrass depth penetration were developed for use as a biological indicator of integrated light availability and long-term trends in water quality. A year-long water quality monitoring programme in Moreton Bay was coupled with a series of seagrass depth transects. A strong gradient between the western (landward) and eastern (seaward) portions of Moreton Bay was observed in both water quality and seagrass depth range. Higher concentrations of chlorophyll a, total suspended solids, dissolved and total nutrients, and light attenuation coefficients in the water column and correspondingly shallower depth limits of the seagrass Zostera capricorni were observed in the western portions of the bay. Relatively high correlation coefficient values (r2 > 0.8) were observed between light attenuation coefficient, total suspended solids, chlorophyll a, total Kjeldahl nitrogen and Zostera capricorni depth range. Low correlation coefficient values (r2 < 0.8) between seagrass depth range and dissolved inorganic nutrients were observed. Seagrasses had disappeared over a five-year period near the mouth of the Logan River, a turbid river with increased land use in its watershed. At a site 9 km from the river mouth, a significant decrease in seagrass depth range corresponded to higher light attenuation, chlorophyll a, total suspended solids and total nitrogen content relative to a site 21 km from the river mouth. Seagrass depth penetration thus appears to be a sensitive bio-indicator of some water quality parameters, with application for water quality management.

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

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.

scholarly journals Population structure and genetic diversity of non-native aoudad populations

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).

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

2019 ◽  
Vol 286 (1916) ◽  
pp. 20191989 ◽  
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.

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

2016 ◽  
Vol 65 (1) ◽  
pp. 59-66 ◽  
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.

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

2021 ◽  
Author(s):  
Gregory Thom ◽  
Camila C. Ribas ◽  
Eduardo Shultz ◽  
Alexandre Aleixo ◽  
Cristina Y. Miyaki
Keyword(s):  
Genetic Diversity ◽  
Spatial Patterns ◽  
Amazon Basin ◽  
Population Connectivity ◽  
Alternative Methods ◽  
Forest Species ◽  
Effective Population ◽  
Habitat Specificity ◽  
Heterogeneous Distribution ◽  
Solimões River

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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