Integrated analysis of the ringneck snake Diadophis punctatus complex (Colubridae: Dipsadidae) in a biodiversity hotspot provides the foundation for conservation reassessment

Abstract Species classification may not reflect the underlying/cryptic genetic diversity and focusing on groups that do not represent historically independent units can misdirect conservation efforts. The identification of evolutionarily significant units (ESUs) allows cryptic genetic diversity to be accounted for when designating conservation priorities. We used multi-locus coalescent-based species delimitation methods and multivariate analyses of morphological data to examine whether the subspecies merit conservation recognition and infer the ESUs in ringneck snakes (Diadophis punctatus) throughout the California Floristic Province. Species delimitation methods failed to recover groups consistent with designated subspecies and instead inferred three well supported, mostly geographically isolated lineages. Divergence time estimates suggest that the divergences were driven by historical isolation associated with Pleistocene climate shifts. We found a correlation between increased morphological differentiation and time since divergence, and greater niche similarity between the more recently diverged eastern California and western California groups. Based on these results, we propose that the morphological similarities are due to a combination of morphological conservatism and evolutionary stasis. Our study provides the foundation necessary to re-assess the biodiversity and conservation status of ringneck snakes and offers an important step in unveiling the diversity within the western portion of the genus’ range.

Download Full-text

New insights into the genetic diversity of the stone crayfish: taxonomic and conservation implications

BMC Evolutionary Biology ◽

10.1186/s12862-020-01709-1 ◽

2020 ◽

Vol 20 (1) ◽

Cited By ~ 2

Author(s):

Leona Lovrenčić ◽

Lena Bonassin ◽

Ljudevit Luka Boštjančić ◽

Martina Podnar ◽

Mišel Jelić ◽

...

Keyword(s):

Genetic Diversity ◽

Species Delimitation ◽

Evolutionary Dynamics ◽

Nuclear Dna ◽

Freshwater Crayfish ◽

Meristic Characters ◽

Data Set ◽

Divergence Time Estimates ◽

Evolutionary Distinctiveness ◽

Stone Crayfish

Abstract Background Austropotamobius torrentium is a freshwater crayfish species native to central and south-eastern Europe, with an intricate evolutionary history and the highest genetic diversity recorded in the northern-central Dinarides (NCD). Its populations are facing declines, both in number and size across its entire range. By extanding current knowledge on the genetic diversity of this species, we aim to assist conservation programmes. Multigene phylogenetic analyses were performed using different divergence time estimates based on mitochondrial and, for the first time, nuclear DNA markers on the largest data set analysed so far. In order to reassess taxonomic relationships within this species we applied several species delimitation methods and studied the meristic characters with the intention of finding features that would clearly separate stone crayfish belonging to different phylogroups. Results Our results confirmed the existence of high genetic diversity within A. torrentium, maintained in divergent phylogroups which have their own evolutionary dynamics. A new phylogroup in the Kordun region belonging to NCD has also been discovered. Due to the incongruence between implemented species delimitation approaches and the lack of any morphological characters conserved within lineages, we are of the opinion that phylogroups recovered on mitochondrial and nuclear DNA are cryptic subspecies and distinct evolutionary significant units. Conclusions Geographically and genetically isolated phylogroups represent the evolutionary legacy of A. torrentium and are highly relevant for conservation due to their evolutionary distinctiveness and restricted distribution.

Download Full-text

Conservation priorities in an endangered estuarine seahorse are informed by demographic history

Scientific Reports ◽

10.1038/s41598-021-83754-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Thomas Kalama Mkare ◽

Bettine Jansen van Vuuren ◽

Peter R. Teske

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Demographic History ◽

Conservation Status ◽

Limited Range ◽

The Other ◽

Conservation Priorities ◽

Population Declines ◽

Term Survival

AbstractHistorical demographic events shape genetic diversity that remains evident in the genomes of contemporary populations. In the case of species that are of conservation concern, this information helps to unravel evolutionary histories that can be critical in guiding conservation efforts. The Knysna seahorse, Hippocampus capensis, is the world’s most endangered seahorse species, and it presently survives in only three estuaries on the South African south coast. Factors that contributed to the species becoming endangered are unclear; additionally, the lack of information on whether the three populations should be managed separately because of potential long-term isolation hampers effective management efforts. In the present study, we reconstructed the seahorses’ demographic history using a suite of microsatellite loci. We found that the largest population (Knysna Estuary) has colonised the other estuaries relatively recently (< 450 years ago), and that its population size is comparatively large and stable. Neither of the other two populations shows signs of long-term reductions in population size. The high conservation status of the species is thus a result of its limited range rather than historical population declines. Our findings indicate that the long-term survival of H. capensis depends primarily on the successful management of the Knysna population, although the other estuaries may serve as reservoirs of genetic diversity.

Download Full-text

Diversity Assessment of Some Sesame (Sesamum indicum L.) Genotypes Cultivated in Northern Ghana Using Morphological and Simple Sequence Repeat (SSR) Markers

Advances in Agriculture ◽

10.1155/2019/6067891 ◽

2019 ◽

Vol 2019 ◽

pp. 1-10 ◽

Cited By ~ 1

Author(s):

Raphael Adu-Gyamfi ◽

Ruth Prempeh ◽

Issahaku Zakaria

Keyword(s):

Genetic Diversity ◽

Plant Height ◽

Ssr Markers ◽

Analysis Of Variance ◽

Morphological Data ◽

Northern Ghana ◽

Land Races ◽

Diversity Assessment ◽

Parental Lines ◽

Number Of Seeds

In Ghana, sesame is cultivated in some districts of northern Ghana. Genotypes cultivated are land races that are low yielding leading to decline in production. There is the need for improvement of these land races to generate high yielding cultivars. Characterization of genetic diversity of the sesame land races will be of great value in assisting in parental lines selection for sesame breeding programmes in Ghana. Twenty-five sesame land races were collected from five districts in northern Ghana noted for sesame cultivation. Seeds collected were planted in three replicates in randomized complete block design and were evaluated for a number of morphological characters. Data collected were subjected to Principal Component Analysis (PCA) and a dendrogram showing similarity between the accessions were drawn. Data on number of capsules per plant, number of seeds per capsule, and plant height at flowering were subjected to analysis of variance using GenStat Discovery Edition 4. Molecular genetic diversity was assessed by using thirty eight SSR markers widely distributed across sesame genome to characterize the materials. Twenty-one out of the 38 primers were polymorphic. Cluster analyses using the Euclidean similarity test and a complete link clustering method were used to make a dendrogram out of the morphological data. Analysis of variance showed that capsule number was significantly different; a range of 54.9 and 146.7 was produced. The number of seeds per capsule varied significantly and the variation between highest and lowest accession in seed production was 33%. Plant height was also significantly different ranging from 60.6 to 94.1 cm. Using morphological traits the accessions clustered into two major groups and two minor groups and variation among accessions were 10-61%. On the other hand, SSR marker-based dendrogram revealed five major and two minor groups. It showed that variation among the accessions was low, 10-20%. Heterozygosity was 0.52, total alleles produced were 410, and average allele per locus was 19.52. Six accessions, C3, C4, S5, W1, W3, and W5 fell in five different clusters in the SSR dendrogram and in six clusters in the morphomolecular based dendrogram. These accessions were noted for high capsule number per plant and seeds number per capsule and are recommended for consideration as potential parental lines for breeding programme for high yield.

Download Full-text

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

Journal of Marine Biology ◽

10.1155/2011/247030 ◽

2011 ◽

Vol 2011 ◽

pp. 1-14 ◽

Cited By ~ 5

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.

Download Full-text

Analysis of genetic diversity and conservation priorities for six north Ethiopian cattle breeds

Journal of Animal Breeding and Genetics ◽

10.1111/j.1439-0388.2007.00660.x ◽

2007 ◽

Vol 124 (4) ◽

pp. 236-241 ◽

Cited By ~ 11

Author(s):

M. Zerabruk ◽

J. Bennewitz ◽

J. Kantanen ◽

I. Olsaker ◽

O. Vangen

Keyword(s):

Genetic Diversity ◽

Conservation Priorities ◽

Cattle Breeds

Download Full-text

Genetic diversity in Australian Cedar genotypes selected by mixed models

Ciência e Agrotecnologia ◽

10.1590/s1413-70542012000200005 ◽

2012 ◽

Vol 36 (2) ◽

pp. 171-179 ◽

Cited By ~ 1

Author(s):

Rulfe Tavares ◽

Alexandre Pio Viana ◽

Deborah Guerra Barroso ◽

Antonio Teixeira do Amaral Júnior

Keyword(s):

Genetic Diversity ◽

Mixed Models ◽

Forest Products ◽

Raw Material ◽

Morphological Data ◽

Technical Improvement ◽

Diameter At Breast Height ◽

Breast Height ◽

Toona Ciliata ◽

Increasing Demand

The increasing demand for raw material for multiple uses of forest products and by-products has attracted the interest for fast growing species, such as the Australian Cedar (Toona ciliata), which presents high productive and economic potential. The present work aimed at estimating genetic diversity by DNA markers and morphological traits supported for the mixed models. The following traits were measured and genotypes were sampled randomly in different areas: diameter at breast height, height, cylindrical volume, diameter, distance between nodes and crown diameter. Twelve RAPD primers were used and generated a total of 91 marks, 82 of which were polymorphic. The high percentage of polymorphic markers, 90.10%, demonstrated that discrimination in this species is efficient, but it yet little studied, for this case we can find the extent of the genetic basis for the application of technical improvement. The assessment of genetic diversity by the UPGMA method using the binary and morphological data provided the expression of genetic dissimilarities among the accessions evaluated, optimizing the perception of this divergence. The use of mixed models was efficient to assess combined genetic diversity to optimize the selection of genotypes with divergent genetic values for diameter at breast height.

Download Full-text

Microsatellite genotyping from faeces of Lontra longicaudis from southern Brazil

Iheringia Série Zoologia ◽

10.1590/s0073-47212009000100001 ◽

2009 ◽

Vol 99 (1) ◽

pp. 5-11 ◽

Cited By ~ 3

Author(s):

Laura I. Weber ◽

Cintia G. Hildebrand ◽

Anderson Ferreira ◽

Gustavo Pedarassi ◽

José A. Levy ◽

...

Keyword(s):

Genetic Diversity ◽

Conservation Status ◽

Significant Degree ◽

Southern Brazil ◽

High Genetic Diversity ◽

Low Degree ◽

Faecal Samples ◽

High Level ◽

Degree Of Differentiation ◽

Lontra Longicaudis

A genetic study of the neotropical river otter Lontra longicaudis (Olfers, 1818), which has an unknown conservation status, was carried out at the Taim Ecological Station and the margins of the Vargas stream, Rio Grande do Sul, southern Brazil. Faecal samples were collected, and DNA was extracted using a silica-guanidine method. Five microsatellite loci were amplified using PCR with heterologous primers previously described for Lutra lutra (Linnaeus, 1758). Sixteen faecal samples out of 29 from Taim and 11 out of 14 from Vargas stream margins contained enough DNA for genetic analysis. A total of 49 different alleles were found at both localities, from which 18 were exclusively found in individuals from Taim and 17 were exclusives from Vargas individuals. The most common allele was the same at both locations for three loci (Lut715, Lut733, and Lut818). A high level of genetic diversity was found at both sites (NeTaim=4.1, HoTaim=0.299, HeTaim=0.681; NeVargas=4.9, HoVargas=0.355, HeVargas=0.724), being higher at the Vargas stream site. A high and significant level of heterozygote deficiency was observed at most loci according to the χ2 test. The homogeneity χ2 test (P<0.001) showed that there were significant differences in the allele frequencies between the two locations. Genotyping for more than one locus was possible in 81.5% of samples, from which only 37% were possible to genotype for more than three loci. A low degree of relatedness was found among individuals from Taim (R=0.055±0.310), but an even lower value of relatedness was found at the Vargas site (R= -0.285±0.440). The significant degree of differentiation (I=0.890; F ST=0.059) found between Taim and Vargas individuals suggests that there is more than one population of otters in the southern extreme of Brazil, which probably are associated with the water body systems found in this region, the Mirim and the Caiuvá/Flores/Mangueira Lagoons. The high genetic diversity and low relatedness found at the Vargas stream, lead us to believe that the Vargas stream may be acting as a corridor between these water bodies for otter dispersion.

Download Full-text

Species delimitation and population structure in three Onosma (Boraginaceae) species

Biologia ◽

10.1515/biolog-2015-0151 ◽

2015 ◽

Vol 70 (10) ◽

Author(s):

Masoud Sheidai ◽

Samira Sadeghi ◽

Mahnaz-Arab Ameri ◽

Ahmad-Reza Mehrabeian

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Species Delimitation ◽

Genetic Difference ◽

Morphological Variability ◽

Morphological Diversity ◽

Mantel Test ◽

Geographical Distance ◽

Nj Tree ◽

Issr Molecular Markers

AbstractThe present study aimed to reveal genetic diversity and population structure in three Onosma species i.e., Onosma bulbotrichum DC., O. elwendicum Wettst. and O. sericeum Willd. (Boraginaceae) growing in Iran. This study was performed to check if the ISSR molecular markers could be used in the Onosma species delimitation. We also investigated the infra-specific morphological variability and if we can identify infra-species taxonomic forms. The present study revealed within species genetic and morphological diversity. ISSR data could delimit the studied species as they were separated from each other in NJ tree, maximum parsimony and STRUCTURE analysis. AMOVA and Hickory tests produced significant genetic difference among the studied species. The Mantel test showed no correlation between genetic distance and geographical distance of the populations for all three species. Reticulation analysis and Nm estimation showed gene flow among these populations. We could identify a few ISSR loci that are adaptive. Data obtained can be used in conservation of these medicinal plants in Iran.

Download Full-text

Cryptic Genetic Diversity within the Anopheles nili group of Malaria Vectors in the Equatorial Forest Area of Cameroon (Central Africa)

PLoS ONE ◽

10.1371/journal.pone.0058862 ◽

2013 ◽

Vol 8 (3) ◽

pp. e58862 ◽

Cited By ~ 10

Author(s):

Cyrille Ndo ◽

Frédéric Simard ◽

Pierre Kengne ◽

Parfait Awono-Ambene ◽

Isabelle Morlais ◽

...

Keyword(s):

Genetic Diversity ◽

Central Africa ◽

Forest Area ◽

Malaria Vectors ◽

Equatorial Forest ◽

Cryptic Genetic Diversity

Download Full-text

Assessment of Genetic Diversity of Promising Castor Been (Ricinus communis L.) Genotypes in Nigeria

Notulae Scientia Biologicae ◽

10.15835/nsb11310346 ◽

2019 ◽

Vol 11 (3) ◽

pp. 467-474

Author(s):

Bolaji Zuluqurineen SALIHU ◽

Olamide Ahmed FALUSI ◽

Adeyinka Olufemi ADEPOJU ◽

Ibrahim Wasiu AROLU ◽

Oladipupo Yusuf DAUDU ◽

...

Keyword(s):

Genetic Diversity ◽

Diversity Index ◽

Gene Diversity ◽

Ricinus Communis ◽

Polymorphic Information Content ◽

Block Design ◽

Genetic Material ◽

Morphological Data ◽

Research Attention ◽

Ricinus Communis L

Castor oil plant (Ricinus communis L.) is an important oil crop with little research attention in Nigeria. In the present research, extent of genetic diversity among 20 Nigerian castor genotypes was determined using morphological descriptors and molecular markers. The genotypes were laid out on a randomized complete block design with three replicated plots. Molecular genotyping of the genotypes was carried out using genomic Simple Sequence Repeats (SSR). The genotypes revealed high divergence in seed colour, seed shape, seed mottle, seed caruncle and seed sizes. Seedling establishment varied from 70.18% (in Acc. 006) to 93.25% (Acc. 001) with average mean of 81.53%. Raceme length ranged from 15.90 cm to 29.54 cm with population mean of 20.80 cm. The highest seed yield (1222.98 kg/ha) was recorded in Acc. 001 and the least (611.46 kg/ha) was observed in Acc. 006. Seed oil content varied between 32.15% in Acc. 042 and 54.03% in Acc. 006. Agglomerative cluster dendrogram constructed from morphological data showed random distribution of the genotypes into three cluster groups irrespective of the sources/collection points. The genetic diversity based on SSR Marker Analysis revealed high average expected heterozygosity (0.74), Polymorphic information content (0.68), Nei’s gene diversity index (0.72) and Shannon's Information index (1.43). The dendrogram constructed from molecular data grouped the twenty genotypes into three groups at coefficient of 0.34. From these findings, it showed that the twenty genotypes evaluated are divergent in nature and they could serve as good genetic material for castor breeding in Nigeria.

Download Full-text