scholarly journals Small-Scale Environmental Drivers of Plant Community Structure and Diversity in Neotropical Montane Cloud Forests Harboring Threatened Magnolia dealbata in Southern Mexico

Diversity ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 444
Author(s):  
Reyna Domínguez-Yescas ◽  
José Antonio Vázquez-García ◽  
Miguel Ángel Muñiz-Castro ◽  
Gerardo Hernández-Vera ◽  
Eduardo Salcedo-Pérez ◽  
...  
Keyword(s):  
Cloud Forest ◽  
Conservation Status ◽  
Basal Area ◽  
Environmental Drivers ◽  
Small Scale ◽  
Conservation Priorities ◽  
Principal Coordinates Analysis ◽  
Southern Mexico ◽  
Principal Coordinates ◽  
Magnolia Dealbata

Gradient analysis was used to determine factors driving small-scale variation of cloud forest communities harboring Magnolia dealbata, a threatened species and bioculturally relevant tree for the Chinantecan, Mazatecan, Nahuan, and Zapotecan ethnicities in southern Mexico. Particularly, we aimed to: (a) determine factors explaining major community gradients at different heterogeneity scales along a small-scale elevational gradient, (b) test the Decreasing and the Continuum hypotheses along elevation, and (c) classify vegetation to assist in identifying conservation priorities. We used a stratified random sampling scheme for 21 woody stands along a small-scale (352 m) elevational transect. Four main data matrices were used (presence-absence, density, basal area, and guild data). Through Non-metric Multidimensional Scaling (NMS), Principal Coordinates Analysis (PCoA), and distance-based Redundancy Analysis (db-RDA), we found that major community variation was explained by soil pH, displaying an outstanding vegetation discontinuity, separating the species-rich relic Oreomunnea-Ticodendron-stands from stands with higher importance values for M. dealbata. The high species richness observed was explained by a combination of the windward effect of dry-seasonal maximum cloud condensation gain and habitat differentiation-specialization, a phenomenon that may also explain the mid-peak hypothesis and ensure the survival of relic species. Sampling-truncation and conservation status also played a role in this. Our results do not support the Decreasing and Continuum hypotheses along elevation.

scholarly journals La familia Lauraceae en el sur de México: Diversidad, distribución y estado de conservación

2017 ◽  
pp. 59
Author(s):  
Francisco G. Lorea-Hernández
Keyword(s):  
Endemic Species ◽  
Rain Forest ◽  
Tropical Rain Forest ◽  
Cloud Forest ◽  
Conservation Status ◽  
Nature Reserves ◽  
Southern Mexico ◽  
The Family

A survey of the diversity, distribution, and conservation status of the family Lauraceae in southern Mexico was conducted. The diversity account resulted in a list of 120 species representing 10 genera: Aiouea, Beilschmiedia, Cassytha, Cinnamomum, Licaria, Litsea, Mocinnodaphne, Nectandra, Ocotea and Persea. The states of Chiapas, Oaxaca, and Veracruz have the largest numbers of species, particularly for the cloud forest and the tropical rain forest. Endemic species account for 47.5% of the surveyed taxa, which concentrate in Chiapas, Oaxaca, and Veracruz. Only 58 of the species considered in the study are present in the system of nature reserves in southern Mexico. The general implications of these findings for the persistence of this component of the Mexican flora are discussed.

scholarly journals Genotyping of Two Mediterranean Trout Populations in Central-Southern Italy for Conservation Purposes Using a Rainbow-Trout-Derived SNP Array

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1803
Author(s):  
Valentino Palombo ◽  
Elena De Zio ◽  
Giovanna Salvatore ◽  
Stefano Esposito ◽  
Nicolaia Iaffaldano ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Genetic Structure ◽  
Fishery Management ◽  
Snp Array ◽  
Fine Scale ◽  
Principal Coordinates Analysis ◽  
Data Set ◽  
Management Actions ◽  
Principal Coordinates ◽  
Mediterranean Trout

Mediterranean trout is a freshwater fish of particular interest with economic significance for fishery management, aquaculture and conservation biology. Unfortunately, native trout populations’ abundance is significantly threatened by anthropogenic disturbance. The introduction of commercial hatchery strains for recreation activities has compromised the genetic integrity status of native populations. This work assessed the fine-scale genetic structure of Mediterranean trout in the two main rivers of Molise region (Italy) to support conservation actions. In total, 288 specimens were caught in 28 different sites (14 per basins) and genotyped using the Affymetrix 57 K rainbow-trout-derived SNP array. Population differentiation was analyzed using pairwise weighted FST and overall F-statistic estimated by locus-by-locus analysis of molecular variance. Furthermore, an SNP data set was processed through principal coordinates analysis, discriminant analysis of principal components and admixture Bayesian clustering analysis. Firstly, our results demonstrated that rainbow trout SNP array can be successfully used for Mediterranean trout genotyping. In fact, despite an overwhelming number of loci that resulted as monomorphic in our populations, it must be emphasized that the resulted number of polymorphic loci (i.e., ~900 SNPs) has been sufficient to reveal a fine-scale genetic structure in the investigated populations, which is useful in supporting conservation and management actions. In particular, our findings allowed us to select candidate sites for the collection of adults, needed for the production of genetically pure juvenile trout, and sites to carry out the eradication of alien trout and successive re-introduction of native trout.

scholarly journals Conservation Status of Marine Biodiversity in Oceania: An Analysis of Marine Species on the IUCN Red List of Threatened Species

2011 ◽  
Vol 2011 ◽  
pp. 1-14 ◽  
Author(s):  
Beth A. Polidoro ◽  
Cristiane T. Elfes ◽  
Jonnell C. Sanciangco ◽  
Helen Pippard ◽  
Kent E. Carpenter
Keyword(s):  
Threatened Species ◽  
Environmental Changes ◽  
Extinction Risk ◽  
Conservation Status ◽  
Marine Species ◽  
Iucn Red List ◽  
Red List ◽  
Marine Biodiversity ◽  
Conservation Priorities ◽  
Conservation Action

Given the economic and cultural dependence on the marine environment in Oceania and a rapidly expanding human population, many marine species populations are in decline and may be vulnerable to extinction from a number of local and regional threats. IUCN Red List assessments, a widely used system for quantifying threats to species and assessing species extinction risk, have been completed for 1190 marine species in Oceania to date, including all known species of corals, mangroves, seagrasses, sea snakes, marine mammals, sea birds, sea turtles, sharks, and rays present in Oceania, plus all species in five important perciform fish groups. Many of the species in these groups are threatened by the modification or destruction of coastal habitats, overfishing from direct or indirect exploitation, pollution, and other ecological or environmental changes associated with climate change. Spatial analyses of threatened species highlight priority areas for both site- and species-specific conservation action. Although increased knowledge and use of newly available IUCN Red List assessments for marine species can greatly improve conservation priorities for marine species in Oceania, many important fish groups are still in urgent need of assessment.

scholarly journals Tree Species Diversity and Composition of Miombo Woodlands in South-Central Angola: A Chronosequence of Forest Recovery after Shifting Cultivation

2017 ◽  
Vol 2017 ◽  
pp. 1-13 ◽  
Author(s):  
Francisco M. P. Gonçalves ◽  
Rasmus Revermann ◽  
Amândio L. Gomes ◽  
Marcos P. M. Aidar ◽  
Manfred Finckh ◽  
...  
Keyword(s):  
Shifting Cultivation ◽  
Stand Structure ◽  
Woody Species ◽  
Distinct Group ◽  
Forest Recovery ◽  
Miombo Woodlands ◽  
Principal Coordinates Analysis ◽  
South Central ◽  
Principal Coordinates ◽  
Management Plans

The study was carried out in the Cusseque area of the Municipality of Chitembo in south-central Angola. Our objectives were to assess the floristic diversity, the species composition, and stand structure of Miombo woodlands during regeneration after shifting cultivation. A total of 40 plots of 1000 m2were surveyed and analyzed, corresponding to mature forests/woodlands and three fallow types of different age. The analyses were based on plot inventories of all trees with DBH ≥ 5 cm. A total of 51 woody species, 38 genera, and 19 families were recorded. The dominant family was Fabaceae, with subfamily Caesalpinioideae being very abundant. Shannon Diversity and Evenness were highest in mature forests and young fallows, while the mature forest stands showed the highest species richness. A Principal Coordinates Analysis (PCoA) showed many species shared between the intermediate fallow types, but only few species were shared with young fallows. Mature forests formed a clearly distinct group. This study shows potential pathways of forest recovery in terms of faster regeneration after agricultural abandonment and, thus, the results presented here can be used in future conservation and management plans in order to reduce the pressure on mature forests.

scholarly journals Unraveling city-specific signature and identifying sample origin locations for the data from CAMDA MetaSUB challenge

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Runzhi Zhang ◽  
Alejandro R. Walker ◽  
Susmita Datta
Keyword(s):  
Machine Learning ◽  
Error Rates ◽  
Average Error ◽  
Importance Score ◽  
Learning Methods ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Total Variability ◽  
The Common ◽  
Feature Selecting

Abstract Background Composition of microbial communities can be location-specific, and the different abundance of taxon within location could help us to unravel city-specific signature and predict the sample origin locations accurately. In this study, the whole genome shotgun (WGS) metagenomics data from samples across 16 cities around the world and samples from another 8 cities were provided as the main and mystery datasets respectively as the part of the CAMDA 2019 MetaSUB “Forensic Challenge”. The feature selecting, normalization, three methods of machine learning, PCoA (Principal Coordinates Analysis) and ANCOM (Analysis of composition of microbiomes) were conducted for both the main and mystery datasets. Results Features selecting, combined with the machines learning methods, revealed that the combination of the common features was effective for predicting the origin of the samples. The average error rates of 11.93 and 30.37% of three machine learning methods were obtained for main and mystery datasets respectively. Using the samples from main dataset to predict the labels of samples from mystery dataset, nearly 89.98% of the test samples could be correctly labeled as “mystery” samples. PCoA showed that nearly 60% of the total variability of the data could be explained by the first two PCoA axes. Although many cities overlapped, the separation of some cities was found in PCoA. The results of ANCOM, combined with importance score from the Random Forest, indicated that the common “family”, “order” of the main-dataset and the common “order” of the mystery dataset provided the most efficient information for prediction respectively. Conclusions The results of the classification suggested that the composition of the microbiomes was distinctive across the cities, which could be used to identify the sample origins. This was also supported by the results from ANCOM and importance score from the RF. In addition, the accuracy of the prediction could be improved by more samples and better sequencing depth.

Monitoring of small rock pools reveals differential effects of chronic anthropogenic disturbance on birds and mammals in the Calakmul region, southern Mexico

2021 ◽  
pp. 1-10
Author(s):  
Carlos M. Delgado-Martínez ◽  
Fredy Alvarado ◽  
Melanie Kolb ◽  
Eduardo Mendoza
Keyword(s):  
Species Richness ◽  
Anthropogenic Disturbance ◽  
Forest Cover ◽  
Biosphere Reserve ◽  
Bird Diversity ◽  
Small Scale ◽  
Rock Pools ◽  
Southern Mexico ◽  
Wildlife Species ◽  
The Impact

Abstract Great attention has been drawn to the impacts of habitat deforestation and fragmentation on wildlife species richness. In contrast, much less attention has been paid to assessing the impacts of chronic anthropogenic disturbance on wildlife species composition and behaviour. We focused on natural small rock pools (sartenejas), which concentrate vertebrate activity due to habitat’s water limitation, to assess the impact of chronic anthropogenic disturbance on the species richness, diversity, composition, and behaviour of medium and large-sized birds and mammals in the highly biodiverse forests of Calakmul, southern Mexico. Camera trapping records of fauna using sartenejas within and outside the Calakmul Biosphere Reserve (CBR) showed that there were no effects on species richness, but contrasts emerged when comparing species diversity, composition, and behaviour. These effects differed between birds and mammals and between species: (1) bird diversity was greater outside the CBR, but mammal diversity was greater within and (2) the daily activity patterns of birds differed slightly within and outside the CBR but strongly contrasted in mammals. Our study highlights that even in areas supporting extensive forest cover, small-scale chronic anthropogenic disturbances can have pervasive negative effects on wildlife and that these effects contrast between animal groups.

Genetic analysis of a heritage variety collection

2018 ◽  
Vol 17 (03) ◽  
pp. 232-244 ◽  
Author(s):  
J. M. Preston ◽  
B. V. Ford-Lloyd ◽  
L. M. J. Smith ◽  
R. Sherman ◽  
N. Munro ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Group Method ◽  
Niche Markets ◽  
Principal Coordinates Analysis ◽  
Pair Group ◽  
Landrace Diversity ◽  
Principal Coordinates ◽  
Length Polymorphisms ◽  
Seed Saving ◽  
History Of

AbstractLandraces (including heritage varieties) are an important agrobiodiversity resource offering considerable value as a buffer against crop failures, as a crop for niche markets, and as a source of diversity for crop genetic improvement activities underpinning future food security. Home gardens are reservoirs of landrace diversity, but some of the accessions held in them are vulnerable or threatened with extinction. Those associated with seed saving networks have added security, for example, ca. 800 varieties are stored in the Heritage Seed Library (HSL) of Garden Organic, UK. In this study, Amplified Fragment Length Polymorphisms-based genetic analysis of accessions held in the HSL was used to (a) demonstrate the range of diversity in the collection, (b) characterize accessions to aid collection management and (c) promote broader use of the collection. In total, 171 accessions were included from six crops: Vicia faba L., Pisum sativum L., Daucus carota L., Cucumis sativus L., Lactuca sativa L. and Brassica oleracea L. var. acephala (DC.) Metzq. Average expected heterozygosity ranged from 0.18 to 0.28 in D. carota; 0.02–0.18 in P. sativum; 0.05–0.18 in L. sativa; 0.15–0.26 in B. oleracea var. acephala; 0.15–0.37 in C. sativus and 0.07–0.36 in V. faba. Genetic diversity and Fst values generally reflected the breeding system and cultivation history of the different crops. Comparisons of the diversity found in heritage varieties with that found in commercial varieties did not show a consistent pattern. Principal coordinates analysis and Unweighted Pair Group Method with Arithmetic Mean cluster analysis were used to identify four potential duplicate accession pairs.

Conservation genetics of the endangered Spotted Turtle (Clemmys guttata) illustrate the risks of “bottleneck tests”

2014 ◽  
Vol 92 (2) ◽  
pp. 149-162 ◽  
Author(s):  
Christina M. Davy ◽  
Robert W. Murphy
Keyword(s):  
Population Genetics ◽  
Freshwater Turtles ◽  
Population Declines ◽  
Isolated Populations ◽  
Principal Coordinates Analysis ◽  
Turtle Species ◽  
Principal Coordinates ◽  
Clemmys Guttata ◽  
Spotted Turtle ◽  
Cast Doubt

Studies of population genetics in turtles have suggested that turtles do not experience genetic impacts of bottlenecks as strongly as expected. However, recent studies cast doubt on two commonly used tests implemented in the program BOTTLENECK, suggesting that these findings should be re-evaluated. The Spotted Turtle (Clemmys guttata (Schneider, 1792)) is endangered both globally and within Canada, but genetic data required to develop effective recovery strategies are unavailable. Here, we conducted the first study of population genetic structure in C. guttata. We then used multiple small populations of C. guttata as replicates to test whether the commonly used program BOTTLENECK could detect the genetic signature of bottlenecks in our study populations, which are all thought to have experienced significant declines in the past 2–3 generations (75 years). Turtles (n = 256) were genotyped at 11 microsatellite loci. A suite of Bayesian population genetics analyses and a principal coordinates analysis identified a minimum of 6 distinct genetic populations and a maximum of 10 differentiated subpopulations across the sampled Canadian range of C. guttata, which corresponded to demographically independent units. BOTTLENECK failed to detect population declines. A literature review found that bottleneck tests in 17 of 18 previous genetic studies of tortoises and freshwater turtles were based on suboptimal sampling, potentially confounding their results. High retention of genetic diversity (allelic richness and heterozygosity) in isolated populations of C. guttata and other turtle species is encouraging for species recovery, but conclusions about the prevalence of genetic bottlenecks in such populations should be re-examined.

Use of multivariate methods in forest research site selection

1991 ◽  
Vol 21 (11) ◽  
pp. 1573-1580 ◽  
Author(s):  
Andrew J. Burton ◽  
Carl W. Ramm ◽  
Kurt S. Pregitzer ◽  
David D. Reed
Keyword(s):  
Site Selection ◽  
Large Scale ◽  
Multivariate Methods ◽  
Data Bases ◽  
Principal Coordinates Analysis ◽  
Research Site ◽  
Principal Coordinates ◽  
Alternative Sites ◽  
Existing Data ◽  
Selection Of

In large-scale gradient studies, selection of the best research sites is critical but time-consuming and costly. Multivariate methods can be used to quickly identify suitable sites from existing data bases. Based on a study of acid deposition in the Great Lakes region (the Michigan Gradient Study), we illustrate the use of multivariate methods in screening potential research sites for similarity. Sites were examined using cluster analysis, principal coordinates analysis, and correspondence analysis. The graphical displays generated by the multivariate methods were used to identify similar sites across the gradient. A list of 31 potential sites was reduced to 5 similar research sites and several alternative sites. The results of the multivariate methods compared well with more traditional methods of research site selection but allowed for multiple comparisons of many potential sites using a variety of data from existing data bases. By eliminating sites that are unacceptable with respect to available data, the multivariate methods reduce the number of sites that require field visitation prior to final site verification. This process represents a substantial savings in time and effort when dealing with a long list of potential research sites.

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