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	<title>AMOVA &#8211; Science</title>
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	<title>AMOVA &#8211; Science</title>
	<link>https://scienmag.com</link>
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		<title>Desert Tree&#8217;s Hidden Genetic Map Reveals Isolated Populations Across India&#8217;s Arid Lands</title>
		<link>https://scienmag.com/desert-trees-hidden-genetic-map-reveals-isolated-populations-across-indias-arid-lands/</link>
		
		<dc:creator><![CDATA[Juliet Wilcox]]></dc:creator>
		<pubDate>Tue, 13 Oct 2026 10:24:00 +0000</pubDate>
				<category><![CDATA[Agriculture]]></category>
		<category><![CDATA[AMOVA]]></category>
		<category><![CDATA[arid ecosystems]]></category>
		<category><![CDATA[arid land ecosystem health]]></category>
		<category><![CDATA[conservation genetics]]></category>
		<category><![CDATA[conservation strategies for desert flora]]></category>
		<category><![CDATA[desert ecosystem restoration]]></category>
		<category><![CDATA[Desert Tree genetic diversity]]></category>
		<category><![CDATA[Fabaceae]]></category>
		<category><![CDATA[FST]]></category>
		<category><![CDATA[Genetic diversity]]></category>
		<category><![CDATA[genetic mapping of desert plants]]></category>
		<category><![CDATA[genetic variation in arid zone trees]]></category>
		<category><![CDATA[Gujarat]]></category>
		<category><![CDATA[India desert biodiversity]]></category>
		<category><![CDATA[isolated plant populations in Rajasthan and Gujarat]]></category>
		<category><![CDATA[keystone desert species]]></category>
		<category><![CDATA[Khejri]]></category>
		<category><![CDATA[microsatellite DNA markers]]></category>
		<category><![CDATA[population structure]]></category>
		<category><![CDATA[Prosopis cineraria]]></category>
		<category><![CDATA[Prosopis cineraria conservation]]></category>
		<category><![CDATA[Rajasthan]]></category>
		<category><![CDATA[soil fertility and microclimate regulation]]></category>
		<category><![CDATA[SSR markers]]></category>
		<guid isPermaLink="false">https://scienmag.com/?p=267471</guid>

					<description><![CDATA[A new SSR marker study of 621 Prosopis cineraria trees across 25 populations in Rajasthan and Gujarat reveals strong genetic differentiation among populations, with 65 percent of variation distributed among rather than within populations, underscoring urgent conservation priorities for this keystone desert tree.]]></description>
										<content:encoded><![CDATA[<p>In the parched expanses of Rajasthan and Gujarat, one tree stands as a lifeline for both people and wildlife. Prosopis cineraria, known locally as Khejri and in the Gulf region as Ghaf, is a keystone leguminous tree that anchors entire ecosystems across the arid and semi-arid zones of South Asia and Western Asia. It enriches soil fertility, provides fodder and food, and moderates the harsh microclimate of the desert margins. Yet despite its outsized ecological and socio-economic importance, scientists have long lacked a detailed picture of how genetic variation is distributed across its natural range. A new study published in Plant Biosystems now offers the most comprehensive genetic survey of the species in western India to date, and its findings carry an urgent message for conservation.</p>
<p>Researchers from the Genetics and Tree Improvement Division of the ICFRE-Arid Forest Research Institute in Jodhpur, together with a collaborator from Rungta International Skills University in Bhilai, set out to map the population structure and genetic diversity of P. cineraria using microsatellite markers, commonly called SSR markers. These markers are short, repeating sequences of DNA scattered throughout the genome, and because they mutate rapidly and are inherited in a codominant fashion, they are among the most informative tools available for distinguishing closely related populations. The team sampled an impressive 621 individual trees across 25 populations spanning the states of Rajasthan and Gujarat, capturing the environmental gradient from hyper-arid desert to semi-arid scrubland.</p>
<p>The results, published on 13 October 2026, reveal a species with moderate but meaningful genetic variability. The SSR markers employed showed a polymorphism information content, or PIC, of 0.3526, a value that indicates the markers were moderately informative for detecting genetic differences among individuals. Observed heterozygosity, which measures the proportion of individuals carrying two different versions of a gene at a given locus, ranged from 0.438 to 0.564 across the sampled populations. Expected heterozygosity, a theoretical measure based on allele frequencies, ranged from 0.462 to 0.497. Together, these figures suggest that while the species retains a reservoir of genetic variation, that variation is not evenly or abundantly distributed across its range.</p>
<p>What makes the study striking is not the overall level of diversity but its architecture. Three independent analytical approaches converged on the same conclusion. Bayesian clustering, a statistical method that assigns individuals to genetic groups based on multilocus genotype data, identified three distinct genetic clusters across the sampled range. Principal coordinate analysis, which visualizes genetic distances in a reduced dimensional space, and UPGMA, a hierarchical clustering technique that builds a tree of population relationships, both corroborated this three-cluster structure. The consistency of these methods strengthens confidence that the pattern is real rather than an artifact of any single analytical technique. Notably, the clusters showed evidence of partial admixture, meaning some individuals carry genetic contributions from more than one cluster, hinting at historical gene flow that has since become restricted.</p>
<p>The most dramatic finding came from an analysis of molecular variance, or AMOVA, which partitions genetic variation into components within and among populations. The results showed that 65 percent of the total genetic variation was distributed among populations, while only 35 percent resided within populations. This is an unusual and consequential pattern for a widespread tree species. Many long-lived, outcrossing trees show the opposite tendency, with most variation held within populations because pollen and seed dispersal homogenize gene pools across large areas. The reversal observed here points to a species whose populations have become substantially isolated from one another.</p>
<p>Quantifying that isolation, the researchers calculated a fixation index, FST, of 0.646, a remarkably high value that was statistically significant at P equals 0.001. FST ranges from zero, indicating free interbreeding among populations, to one, indicating complete isolation. A value approaching 0.65 signals severe genetic differentiation, meaning that populations separated by even modest geographic distances have diverged genetically to a striking degree. Restricted gene flow, combined with ecological heterogeneity across the arid to semi-arid gradient and historical dispersal events, appears to have collectively shaped this fragmented genetic landscape, according to the study&#8217;s authors.</p>
<p>The implications for a keystone desert tree are profound. Genetic differentiation of this magnitude means that each population represents a distinct evolutionary unit, carrying unique combinations of alleles that may encode adaptations to local conditions such as soil salinity, temperature extremes, and rainfall variability. If a population is lost, its genetic contribution cannot simply be replaced by translocating trees from elsewhere, because no other population carries the same genetic makeup. This is particularly concerning in the context of climate change, where arid zones are expected to experience intensifying heat and increasingly erratic precipitation. The species&#8217; renowned thermotolerance, highlighted by recent transcriptomic work showing multiple gene families involved in heat stress response, may depend on genetic variants that are unevenly distributed among the fragmented populations.</p>
<p>The study also fills an important gap in the scientific literature. Previous genetic investigations of P. cineraria in India relied on different marker systems, including single primer amplification reactions, gene-targeted markers such as CAAT box-derived polymorphism and start codon targeted polymorphism, and intersimple sequence repeats. A parallel 2025 population genomic study in the United Arab Emirates examined the species in the eastern part of its range. The new SSR-based survey of Rajasthan and Gujarat, funded through the Compensatory Afforestation Fund Management and Planning Authority of India&#8217;s Ministry of Environment, Forest and Climate Change under the National Program for Conservation and Development of Forest Genetic Resources, provides the densest population-level sampling yet conducted in the species&#8217; Indian stronghold.</p>
<p>From a practical standpoint, the findings offer a roadmap for conservation planners. Because most variation lies among populations rather than within them, conservation strategies should prioritize protecting as many distinct populations as possible, particularly those representing each of the three genetic clusters identified by the Bayesian analysis. Seed collection for afforestation and restoration programs should be drawn from multiple populations and matched to local genetic clusters to avoid outbreeding problems and to preserve the adaptive potential embedded in each lineage. The study&#8217;s authors emphasize that the species&#8217; ecological heterogeneity, historical dispersal patterns, and restricted gene flow collectively demand a conservation approach tailored to its fragmented genetic architecture rather than a one-size-fits-all strategy.</p>
<p>Beyond its immediate conservation value, the research contributes to a growing appreciation of desert trees as genetic resources for the future. P. cineraria is increasingly studied as a model for developing stress-tolerant crops, and its genome, published in 2022, has opened doors to understanding how legumes thrive under extreme aridity. The tree&#8217;s pods, leaves, and bark hold nutritional and pharmacological promise, and its role in traditional agroforestry systems across the Thar Desert has sustained agricultural communities for centuries. The iconic Khejri tree is so culturally embedded in Rajasthan that it is protected by community conservation traditions dating back centuries. Safeguarding its genetic diversity, the new study makes clear, is not merely an act of ecological stewardship but an investment in the resilience of dryland agriculture and the millions of people who depend on it. As arid ecosystems face mounting pressure from climate change and land use intensification, detailed genetic maps like this one will become indispensable tools for ensuring that keystone species such as the Khejri tree continue to anchor the deserts they have shaped for millennia.</p>
<p><strong>Subject of Research:</strong> Genetic diversity and population structure of the keystone desert tree Prosopis cineraria in arid and semi-arid India</p>
<p><strong>Article Title:</strong> Population structure and genetic diversity of Prosopis cineraria (Fabaceae) in arid and semi-arid regions of Rajasthan and Gujarat revealed by SSR markers</p>
<p><strong>Article References:</strong> Population structure and genetic diversity of Prosopis cineraria (Fabaceae) in arid and semi-arid regions of Rajasthan and Gujarat revealed by SSR markers. (n.d.). <a href="https://doi.org/10.1007/s44473-026-00280-9" rel="noopener noreferrer">https://doi.org/10.1007/s44473-026-00280-9</a></p>
<p><strong>Image Credits:</strong> AI Generated</p>
<p><strong>DOI:</strong> <a href="https://doi.org/10.1007/s44473-026-00280-9" rel="noopener noreferrer">10.1007/s44473-026-00280-9</a></p>
<p><strong>Keywords:</strong> Prosopis cineraria, SSR markers, genetic diversity, population structure, Khejri, arid ecosystems, conservation genetics, AMOVA, FST, Rajasthan, Gujarat, Fabaceae</p>
]]></content:encoded>
					
		
		
		<post-id xmlns="com-wordpress:feed-additions:1">267471</post-id>	</item>
		<item>
		<title>Moroccan Oases and Atlas Mountains Hide a Surprising Wealth of Fig Tree Genetic Diversity</title>
		<link>https://scienmag.com/moroccan-oases-and-atlas-mountains-hide-a-surprising-wealth-of-fig-tree-genetic-diversity/</link>
		
		<dc:creator><![CDATA[Juliet Wilcox]]></dc:creator>
		<pubDate>Mon, 05 Oct 2026 12:31:40 +0000</pubDate>
				<category><![CDATA[Agriculture]]></category>
		<category><![CDATA[agroecosystems]]></category>
		<category><![CDATA[AMOVA]]></category>
		<category><![CDATA[Atlas Mountains]]></category>
		<category><![CDATA[Atlas Mountains fig cultivars]]></category>
		<category><![CDATA[caprifigs]]></category>
		<category><![CDATA[Ficus carica]]></category>
		<category><![CDATA[fig tree biodiversity in Moroccan regions]]></category>
		<category><![CDATA[Genetic diversity]]></category>
		<category><![CDATA[genetic variation in Ficus carica]]></category>
		<category><![CDATA[germplasm conservation]]></category>
		<category><![CDATA[ISSR marker analysis of fig trees]]></category>
		<category><![CDATA[ISSR markers]]></category>
		<category><![CDATA[local farming practices and fig diversity]]></category>
		<category><![CDATA[molecular markers]]></category>
		<category><![CDATA[molecular study of Moroccan figs]]></category>
		<category><![CDATA[Moroccan fig tree genetic diversity]]></category>
		<category><![CDATA[Morocco]]></category>
		<category><![CDATA[oases]]></category>
		<category><![CDATA[Oases fig tree conservation]]></category>
		<category><![CDATA[plant breeding]]></category>
		<category><![CDATA[plant genetic diversity assessment]]></category>
		<category><![CDATA[preservation of fig genetic resources]]></category>
		<category><![CDATA[regional fig cultivar differences]]></category>
		<category><![CDATA[traditional agroecosystems in Morocco]]></category>
		<guid isPermaLink="false">https://scienmag.com/?p=237996</guid>

					<description><![CDATA[A new ISSR marker study of 93 Moroccan fig cultivars reveals exceptionally high genetic diversity, with 89 percent of variation found within traditional oasis and Atlas Mountain agroecosystems.]]></description>
										<content:encoded><![CDATA[<p>Deep in the oases of southern Morocco and across the rugged slopes of the Atlas Mountains, farmers have tended fig trees for generations without ever thinking of themselves as guardians of a genetic treasure. A new study now confirms that these traditional agroecosystems are doing exactly that. Researchers led by Ibtissam Mardoume of Sultan Moulay Slimane University in Beni Mellal analyzed 93 fig cultivars collected from the Atlas regions and the southern and south-eastern oases of Morocco, and found a level of genetic diversity that surprised even the team behind the work. The findings, published in Plant Biosystems, offer one of the most detailed molecular portraits to date of the fig tree, Ficus carica, in a country that sits at the heart of the species&#8217; historical range.</p>
<p>The team used inter-simple sequence repeat markers, known as ISSR markers, to probe the genomes of the collected trees. ISSR markers target short repeated DNA sequences scattered throughout the genome, amplifying the stretches between them to produce a fingerprint of bands that can be compared across individuals. Because these microsatellite-flanking regions mutate relatively quickly, ISSR markers are sensitive tools for detecting variation even among closely related cultivars of the same crop. In this study, 14 ISSR primers generated 214 scorable bands across the 93 cultivars, and a striking 184 of those bands, or 85.98 percent, were polymorphic, meaning they differed among at least some of the trees sampled.</p>
<p>Those numbers translate into exceptionally high genetic diversity for a cultivated fruit tree. The researchers calculated a resolving power of 8.00 for their marker set, a Nei&#8217;s gene diversity index of 0.34, a polymorphism information content of 0.52, and a Shannon information index of 0.34. Each of these metrics describes a different facet of variation, from how well the markers distinguish individual genotypes to how much uncertainty remains when guessing the genetic makeup of a randomly chosen tree. A PIC value above 0.5 is generally considered highly informative, indicating that the ISSR system captured substantial discriminating power across the Moroccan fig collection.</p>
<p>Perhaps the most consequential finding came from the analysis of molecular variance, or AMOVA, a statistical framework that partitions genetic variation into components within and between groups. The results showed that 89 percent of the total genetic variation resided within groups of cultivars, while only 11 percent was found between groups. In practical terms, this means that a farmer&#8217;s orchard in one valley may contain nearly as much hidden genetic variation as an entire region hundreds of kilometers away. Traditional agroecosystems, where multiple varieties are grown side by side and exchanged informally among neighbors, appear to be incubators of diversity rather than mere repositories of it.</p>
<p>Cluster analysis reinforced this picture of diffuse, locally rich diversity. Using UPGMA, a hierarchical clustering method that groups genotypes according to overall band-sharing similarity, the researchers organized the 93 cultivars into five main groups. The edible female figs from the Beni Mellal-Khenifra region showed particularly high genetic dispersion, scattering across the clustering diagram rather than gathering into a tight regional cluster. That dispersion suggests extensive exchange of planting material, seedling selection by farmers, and possibly multiple historical introductions of fig germplasm into the region, which historically served as a crossroads for trans-Saharan trade routes.</p>
<p>The caprifigs told a very different story. Caprifigs are the male, inedible figs that produce pollen and host the tiny fig wasp, Blastophaga psenes, which pollinates female fig flowers in a symbiosis so ancient and so intimate that neither partner can reproduce without the other. In the study, caprifigs formed a distinct and homogeneous cluster regardless of where they had been collected, separating cleanly from the edible female cultivars. This clear genetic split mirrors the gynodioecious breeding system of Ficus carica, in which male and female functional forms are genetically differentiated, and it validates the use of molecular markers to distinguish caprifig germplasm for breeding and pollination management.</p>
<p>The significance of this work extends well beyond Morocco&#8217;s borders. The fig is one of the oldest domesticated fruit trees in the world, and its center of diversity lies in the Middle East and Mediterranean basin, with Morocco recognized as a rich secondary reservoir. Earlier studies using microsatellite and other marker systems have documented diversity in Turkish, Tunisian, Algerian, and Jordanian fig germplasm, and Moroccan collections have been characterized morphologically and with SSR markers in previous work. What this new study adds is a broad, marker-based survey that explicitly spans both the mountain agroecosystems of the Atlas and the desert oases of the south, two environments that impose very different pressures on the trees growing in them.</p>
<p>That environmental breadth matters for conservation planning. Oases are fragile systems threatened by water scarcity, salinization, and rural depopulation, while mountain terraces face their own pressures from land abandonment and climate shifts. When genetic variation is distributed mostly within rather than between sites, losing any single site erodes a meaningful slice of the species&#8217; total diversity. The authors argue that their results underline the value of ISSR markers for conservation and breeding programs, providing a cost-effective way to identify unique genotypes, avoid duplicating accessions in germplasm collections, and select parents for crosses that maximize genetic gain in fruit quality, drought tolerance, or disease resistance.</p>
<p>The study also fits into a growing body of work by the same research group at Sultan Moulay Slimane University, which has applied ISSR markers to Moroccan walnuts, plums, apples, and the endemic resin spurge Euphorbia resinifera. Together with companion studies by Mardoume and colleagues on the sugar profiles, organic acids, antioxidant activity, and phenotypic variability of Moroccan figs, the molecular data sketch a crop that is not only genetically rich but also chemically and morphologically diverse. For breeders seeking climate-resilient cultivars, such multidimensional diversity is raw material that cannot be recreated once lost.</p>
<p>For now, the message from the oases and mountains of Morocco is a hopeful one: centuries of traditional farming have quietly assembled one of the most genetically diverse fig populations ever surveyed with molecular markers. The challenge ahead is to document and conserve that diversity before the agroecosystems that sustain it disappear. With 85.98 percent of their marker bands polymorphic and nearly nine-tenths of the variation locked within local groups, Moroccan figs demonstrate that the future of food security under global change may depend as much on the smallholdings of traditional farmers as on any high-tech gene bank.</p>
<p><strong>Subject of Research:</strong> Genetic diversity of fig tree (Ficus carica) cultivars and caprifigs in Moroccan oases and Atlas regions assessed with ISSR molecular markers</p>
<p><strong>Article Title:</strong> Genetic diversity of Caprifigs and female fig (Ficus carica) from Moroccan oases and Atlas Regions revealed by ISSR markers</p>
<p><strong>Article References:</strong> Mardoume, I., Bouda, S., Khachtib, Y., Zaggoumi, H., Neg, I., Ait Bella, Y., &amp; Haddioui, A. (2026). Genetic diversity of Caprifigs and female fig (Ficus carica) from Moroccan oases and Atlas Regions revealed by ISSR markers. <em>Plant Biosystems, 160</em>(4), Article 216. <a href="https://doi.org/10.1007/s44473-026-00221-6" rel="noopener noreferrer">https://doi.org/10.1007/s44473-026-00221-6</a></p>
<p><strong>Image Credits:</strong> AI Generated</p>
<p><strong>DOI:</strong> <a href="https://doi.org/10.1007/s44473-026-00221-6" rel="noopener noreferrer">10.1007/s44473-026-00221-6</a></p>
<p><strong>Keywords:</strong> Ficus carica, genetic diversity, ISSR markers, Morocco, caprifigs, oases, Atlas Mountains, AMOVA, agroecosystems, germplasm conservation, plant breeding, molecular markers</p>
]]></content:encoded>
					
		
		
		<post-id xmlns="com-wordpress:feed-additions:1">237996</post-id>	</item>
		<item>
		<title>DNA Barcodes Reveal Hidden Diversity in Nigeria&#8217;s Avocado Genebank</title>
		<link>https://scienmag.com/dna-barcodes-reveal-hidden-diversity-in-nigerias-avocado-genebank/</link>
		
		<dc:creator><![CDATA[Alan Morgan]]></dc:creator>
		<pubDate>Wed, 23 Sep 2026 23:58:46 +0000</pubDate>
				<category><![CDATA[Agriculture]]></category>
		<category><![CDATA[AMOVA]]></category>
		<category><![CDATA[avocado]]></category>
		<category><![CDATA[avocado breeding challenges in tropical regions]]></category>
		<category><![CDATA[Avocado genetic diversity in Nigeria]]></category>
		<category><![CDATA[DNA barcoding for crop conservation]]></category>
		<category><![CDATA[genebank]]></category>
		<category><![CDATA[Genetic diversity]]></category>
		<category><![CDATA[germplasm]]></category>
		<category><![CDATA[heterozygosity and outcrossing in avocado populations]]></category>
		<category><![CDATA[impact of pests and climate change on avocado breeding]]></category>
		<category><![CDATA[ISSR markers]]></category>
		<category><![CDATA[molecular analysis of Nigerian avocado genebank]]></category>
		<category><![CDATA[molecular markers]]></category>
		<category><![CDATA[molecular techniques in plant genetic resource assessment]]></category>
		<category><![CDATA[Nigeria]]></category>
		<category><![CDATA[NIHORT]]></category>
		<category><![CDATA[open-pollinated seed]]></category>
		<category><![CDATA[Persea americana]]></category>
		<category><![CDATA[plant breeding]]></category>
		<category><![CDATA[preserving genetic resources in West Africa]]></category>
		<category><![CDATA[role of genebanks in maintaining crop biodiversity]]></category>
		<category><![CDATA[SCoT markers]]></category>
		<category><![CDATA[significance of Nigeria's avocado germplasm]]></category>
		<category><![CDATA[smallholder farmers' contribution to avocado collections]]></category>
		<guid isPermaLink="false">https://scienmag.com/?p=211430</guid>

					<description><![CDATA[Using ISSR and SCoT DNA markers, Nigerian researchers have mapped moderate genetic diversity across fifteen avocado accessions from the NIHORT genebank, finding that nearly all variation lies within rather than between geographic groupings.]]></description>
										<content:encoded><![CDATA[<p>Avocados have conquered the world. Global production of the creamy green fruit has tripled since 2000, reaching roughly 19 billion pounds by 2021, driven by consumer enthusiasm for its healthy fats, fibre, vitamins and minerals. Yet behind the global boom lies a quieter scientific challenge: preserving the genetic raw material that will allow breeders to keep the crop productive in the face of pests, diseases and a changing climate. A new study from Nigeria now offers a detailed molecular snapshot of one of West Africa&#8217;s most important avocado collections, and its findings carry lessons for genebanks everywhere.</p>
<p>Researchers at the National Horticultural Research Institute (NIHORT) in Ibadan set out to assess the genetic diversity of fifteen avocado accessions conserved in the institute&#8217;s genebank. The seeds behind these accessions were originally collected from smallholder farmers across four states in south-eastern Nigeria — Imo, Enugu, Anambra and Abia — during successive collection missions, and were registered with NIHORT accession numbers upon entry into the genebank. Because avocado is highly heterozygous and predominantly outcrossing, with a protogynous–protandrous flowering system that promotes cross-pollination, the seedlings raised from these seeds represent open-pollinated half-sib progenies rather than clones of the maternal trees, and were treated as independent accessions in the analysis.</p>
<p>The team, led by Omolara I. Akinyoola and published in the journal Discover Plants, employed two complementary DNA marker systems: inter-simple sequence repeats (ISSR) and start codon targeted (SCoT) markers. ISSR primers amplify DNA fragments lying between simple sequence repeats in the genome and require no prior knowledge of the species&#8217; DNA sequence, making them accessible and inexpensive. SCoT markers, first developed in rice by Collard and Mackill, target regions surrounding the start codons of genes, giving them a functional bias that often makes them more informative. After a pilot screen of twenty ISSR and fifteen SCoT primers on three representative accessions, the researchers selected five primers of each type based on band clarity, polymorphism and reproducibility.</p>
<p>The laboratory work began with fresh young leaflets collected from the field and preserved in liquid nitrogen. Genomic DNA was extracted from approximately 100 milligrams of leaf tissue per accession using a modified CTAB protocol, in which polyvinylpyrrolidone and 2-mercaptoethanol were added to suppress polyphenols and oxidation, and the chloroform–isoamyl alcohol extraction step was repeated twice to remove residual protein and lipid. DNA was precipitated overnight with ice-cold isopropanol, washed with 70 percent ethanol and re-suspended in buffer containing RNase A. Quality checks on 1 percent agarose gels confirmed sharp, high-molecular-weight bands with no shearing, and Nanodrop spectrophotometry gave A260/A280 purity ratios between 1.80 and 2.00 before samples were diluted to a working concentration of 30 nanograms per microlitre.</p>
<p>Polymerase chain reactions were carried out in 25-microlitre volumes on an Applied Biosystems GeneAmp 9700 thermal cycler. ISSR amplification used a touchdown profile in which the annealing temperature dropped from 65 to 56 degrees Celsius over ten cycles before thirty standard cycles at 55 degrees, while SCoT amplification used thirty-five cycles with a 50-degree annealing temperature. Amplified fragments were separated on 2 percent agarose gels, visualised under ultraviolet transillumination and scored manually against a 50-base-pair ladder, with faint or ambiguous bands excluded. The convergence of results across two independent marker systems, and across multiple analysis platforms, provided a form of internal validation that strengthens confidence in the findings.</p>
<p>The results revealed a moderate but meaningful reservoir of variation. The ten loci detected a total of 41 polymorphic alleles, averaging 4.1 alleles per locus — higher than the 3.1 alleles per locus reported in a previous avocado study using EST-SSR primers. The polymorphism information content, a measure of a locus&#8217;s discriminating power, ranged from 0.509 to 0.825 with a mean of 0.654, and gene diversity averaged 0.708 across the ten loci. Genetic similarity coefficients between accessions ranged from 0.59 to 0.84. Notably, SCoT markers outperformed ISSR markers, generating a higher mean number of alleles per locus (4.4 versus 3.8) and higher mean PIC values (0.671 versus 0.637), leading the authors to recommend the combined use of both systems rather than either alone.</p>
<p>When the researchers clustered the accessions using the unweighted pair group method with arithmetic mean (UPGMA) on Jaccard dissimilarities, supported by 1000 bootstrap resamplings, the fifteen accessions split into two main clusters — one containing six accessions and the other nine — with membership broadly reflecting the south-eastern states of origin. A factorial coordinate analysis performed in DARwin software resolved four geographic groups along the first two factorial axes, with groups dominated respectively by accessions from Imo, Enugu and Anambra, while the single Abia accession stood apart. Some accessions, however, were interwoven between groups, a pattern the authors attribute to informal farmer-to-farmer seed exchange across state boundaries.</p>
<p>The most striking result came from the analysis of molecular variance. AMOVA partitioned 99.3 percent of the genetic variation within the UPGMA clusters and only 0.7 percent between them, with a Phi statistic of 0.007 that was statistically non-significant (P = 0.395, based on 9999 random permutations). Cross-validation in a second R package yielded an essentially identical result (P = 0.390), confirming the robustness of the partitioning. In other words, the two clusters represent dissimilarity gradients within a single, largely panmictic gene pool rather than genetically isolated subpopulations. The authors attribute this to two interacting forces: avocado&#8217;s strongly outcrossing reproductive biology, which maintains high heterozygosity within genotypes, and widespread informal seed exchange among smallholder farmers, which has homogenised allele frequencies across the sampled states.</p>
<p>The study is not without limitations, which the authors acknowledge candidly. The sample of fifteen accessions, while reflecting the current holdings of the NIHORT avocado germplasm at the time of sampling, is modest for inferring fine-scale population structure and limits the statistical power of subgroup analyses. Marker-trait associations were not pursued, and the dominant nature of ISSR and SCoT markers means each accession had to be treated as a single haploid genotype. Future work, the team suggests, should integrate SNP-based platforms such as genotyping-by-sequencing with phenotypic and biochemical fruit characterisation, to link the genetic variation documented here to agronomically relevant traits such as fruit quality, pest resistance and climate resilience.</p>
<p>Even so, the significance of the work extends well beyond a single genebank. Nigeria&#8217;s avocado industry is growing rapidly and holds considerable potential in the global market, but it faces threats from pests including the avocado lace bug, the Persea mite and the western avocado leaf roller, as well as diseases such as anthracnose and avocado black streak. The moderate diversity documented in the NIHORT collection provides a baseline molecular dataset for future curation, hybridisation and selection, and underscores a broader truth for crop science: genetic diversity is the raw currency of breeding, and knowing exactly what a genebank holds is the first step towards spending it wisely. The identified variation can now be deployed in breeding programmes aimed at developing better varieties with desirable traits, while the finding that most variation lies within rather than between geographic groupings offers a caution against assuming that provenance alone guarantees genetic distinctiveness in conserved germplasm.</p>
<p><strong>Subject of Research:</strong> Genetic diversity assessment of avocado germplasm using ISSR and SCoT molecular markers</p>
<p><strong>Article Title:</strong> Genetic diversity assessment of avocado (Persea americana Mill.) germplasm from NIHORT genebank</p>
<p><strong>Article References:</strong> Akinyoola, O. I., Olagunju, Y. O., Matthew, J. O., Akin-Idowu, P. E., &amp; Ajayi, E. O. (2026). Genetic diversity assessment of avocado (Persea americana Mill.) germplasm from NIHORT genebank. <em>Discover Plants, 3</em>(1), Article 414. <a href="https://doi.org/10.1007/s44372-026-00866-9" rel="noopener noreferrer">https://doi.org/10.1007/s44372-026-00866-9</a></p>
<p><strong>Image Credits:</strong> AI Generated</p>
<p><strong>DOI:</strong> <a href="https://doi.org/10.1007/s44372-026-00866-9" rel="noopener noreferrer">10.1007/s44372-026-00866-9</a></p>
<p><strong>Keywords:</strong> avocado, Persea americana, genetic diversity, ISSR markers, SCoT markers, germplasm, genebank, Nigeria, NIHORT, molecular markers, AMOVA, plant breeding</p>
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		<post-id xmlns="com-wordpress:feed-additions:1">211430</post-id>	</item>
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		<title>DNA Hints at Hidden Diversity in a Declining South Asian Frog</title>
		<link>https://scienmag.com/dna-hints-at-hidden-diversity-in-a-declining-south-asian-frog/</link>
		
		<dc:creator><![CDATA[Juliet Wilcox]]></dc:creator>
		<pubDate>Sat, 12 Sep 2026 16:06:39 +0000</pubDate>
				<category><![CDATA[Biology]]></category>
		<category><![CDATA[16S rRNA]]></category>
		<category><![CDATA[AMOVA]]></category>
		<category><![CDATA[amphibian biodiversity assessment]]></category>
		<category><![CDATA[amphibian conservation]]></category>
		<category><![CDATA[color polymorphism]]></category>
		<category><![CDATA[cryptic amphibian diversity]]></category>
		<category><![CDATA[cryptic species]]></category>
		<category><![CDATA[cryptic species identification]]></category>
		<category><![CDATA[DNA analysis of frog populations]]></category>
		<category><![CDATA[frog color morphotypes]]></category>
		<category><![CDATA[Genetic diversity]]></category>
		<category><![CDATA[genetic diversity in declining species]]></category>
		<category><![CDATA[global amphibian conservation efforts]]></category>
		<category><![CDATA[habitat degradation]]></category>
		<category><![CDATA[habitat-specific frog genetics]]></category>
		<category><![CDATA[impact of habitat degradation on amphibians]]></category>
		<category><![CDATA[molecular ecology]]></category>
		<category><![CDATA[molecular techniques in herpetology]]></category>
		<category><![CDATA[phylogenetics]]></category>
		<category><![CDATA[RAG-1]]></category>
		<category><![CDATA[South Asia]]></category>
		<category><![CDATA[South Asian amphibian decline]]></category>
		<category><![CDATA[South Asian frog conservation]]></category>
		<category><![CDATA[Sphaerotheca maskeyi]]></category>
		<guid isPermaLink="false">https://scienmag.com/?p=196135</guid>

					<description><![CDATA[A new genetic study of the cryptic South Asian frog Sphaerotheca maskeyi finds high within-population diversity, no significant divergence between its color forms, and subtle signs of erosion in degraded habitats.]]></description>
										<content:encoded><![CDATA[<p>Across the flooded fields and scrubby foothills of South Asia lives a frog that most people, including many biologists, would struggle to tell apart from its close relatives. The burrowing frog Sphaerotheca maskeyi, a medium-sized member of the family Dicroglossidae, is a master of anonymity: its external appearance varies so subtly that field researchers have long puzzled over whether the animals they catch represent one population, several, or something more. Now, a new genetic study has peered beneath the skin of this cryptic amphibian, using DNA to map how its diversity is distributed across different habitats and across two distinct color forms, and the results carry important implications for how this declining species should be conserved.</p>
<p>The research, conducted by an international team of scientists working at Pir Mehr Ali Shah Arid Agriculture University Rawalpindi in Pakistan, Nanjing Forestry University in China, and Purdue University in the United States, set out to answer three fundamental questions. First, where does S. maskeyi sit on the amphibian tree of life? Second, does the genetic makeup of its populations differ between natural and degraded habitats? And third, do the two recognized morphotypes of the species, known as the dotted form and the rusty form, represent genetically distinct lineages? To answer these questions, the team sequenced two widely used genetic markers: a segment of the mitochondrial 16S ribosomal RNA gene, which accumulates mutations quickly and is a workhorse for species-level identification, and a portion of the nuclear RAG-1 gene, which evolves more slowly and provides an independent check on mitochondrial results.</p>
<p>The phylogenetic analyses left little room for doubt about species identity. Using both maximum likelihood and Bayesian inference, two complementary statistical frameworks for reconstructing evolutionary trees, the researchers found that every sampled individual clustered firmly within the Sphaerotheca maskeyi clade, clearly separated from other species in the genus. This matters because cryptic morphology often hides cryptic species, and misidentification in the field can quietly corrupt decades of ecological data. By anchoring the species&#8217; genetic identity with two independent markers, the study provides a reliable baseline for all future work on this frog, from population monitoring to taxonomic revision.</p>
<p>The habitat comparison revealed a pattern that is both encouraging and cautionary. Frogs captured in natural habitats showed numerically higher genetic diversity than those from degraded environments. For the mitochondrial 16S marker, natural-habitat populations displayed haplotype diversity of 0.963 and nucleotide diversity of 0.063, compared with 0.760 and 0.054 in degraded habitats. The nuclear RAG-1 gene told a similar story, with haplotype diversity of 0.9818 and nucleotide diversity of 0.0237 in natural settings versus 0.9556 and 0.0175 in degraded ones. Yet when the team ran formal statistical tests, these differences fell short of significance. The pattern is consistent with the idea that habitat degradation erodes genetic variation, a phenomenon documented in many amphibians, but the sample sizes in this study were not sufficient to prove it conclusively.</p>
<p>One of the most consequential findings came from the analysis of molecular variance, or AMOVA, a technique that partitions genetic variation into components occurring among populations versus within them. For both markers, the vast majority of variation was found within populations rather than between them. In practical terms, this means that individual populations of S. maskeyi are not sharply isolated from one another, at least across the geographic scale sampled. High within-population diversity combined with low among-population differentiation can indicate recent shared ancestry, ongoing or historical gene flow, or simply insufficient time for lineages to diverge. For a species whose global population is trending downward, this connectivity is good news in the short term, because it suggests that local extinctions might still be offset by recolonization from neighboring populations.</p>
<p>The comparison between the two morphotypes produced perhaps the most intriguing result of the study. The rusty form and the dotted form look different enough that researchers routinely sort them in the field, but the genetics suggest that appearance is not destiny. The rusty form showed numerically higher nucleotide diversity at both loci, with values of 0.00210 for 16S rRNA and 0.01258 for RAG-1, against 0.00059 and 0.00517 for the dotted form. Intriguingly, the two forms traded the top spot for haplotype diversity depending on the marker: the dotted form reached 1.000 at 16S while the rusty form hit 1.000 at RAG-1. The AMOVA between morphotypes yielded an FST of 0.09057 with a p-value of 0.058, a figure that sits tantalizingly close to the conventional significance threshold but does not cross it. The authors interpret this as weak genetic structuring with no strong evidence of pronounced divergence between the forms.</p>
<p>This near-miss raises a fascinating evolutionary question: if the two morphotypes are not genetically distinct species or deeply separated lineages, what maintains their visual differences? Color polymorphisms in frogs are often maintained by natural selection, sexual selection, or a balance of the two, and recent research has shown that such polymorphisms can persist for millions of years without accompanying genetic divergence across the rest of the genome. It is entirely possible that the dotted and rusty forms of S. maskeyi represent ecologically or reproductively relevant variants shaped by their environments rather than independently evolving lineages. Testing this hypothesis would require genome-wide markers, larger samples, and behavioral or ecological data linking the morphotypes to differences in survival, mating success, or habitat use.</p>
<p>The conservation stakes of this work are considerable. Genetic diversity is the raw material that allows populations to adapt to changing environments, and its loss often precedes, and predicts, demographic collapse. Species with low genetic diversity are more vulnerable to disease outbreaks, climate extremes, and inbreeding depression, threats that are particularly acute for amphibians, the most imperiled class of vertebrates on Earth. Although S. maskeyi is currently classified as Least Concern by the IUCN Red List, its global population trend is declining, and habitat loss across South Asia continues at a relentless pace. The finding that frogs in degraded habitats carry numerically reduced diversity, even if not yet statistically significant, is a warning sign that should not be ignored.</p>
<p>The study also underscores the value of combining mitochondrial and nuclear markers. Mitochondrial DNA, inherited only through mothers, can be swayed by historical demographic events and female-mediated gene flow, while nuclear genes like RAG-1 reflect the blending of ancestry from both sexes. When both markers agree, as they did here, confidence in the conclusions rises substantially. The sequence data from this study, deposited in GenBank under accession numbers PX645625 through PX645652 for 16S rRNA and PX657352 through PX657361 for RAG-1, will serve as a permanent genetic reference for the species and a foundation for future genomic studies.</p>
<p>For now, the message of this research is one of cautious reassurance paired with urgent vigilance. Sphaerotheca maskeyi still harbors substantial genetic diversity across its range, its populations remain genetically connected, and its two color forms are almost certainly variations on a single evolutionary theme rather than separate species. But declining populations and shrinking habitats are silently chipping away at that diversity, and the statistical trends detected in this study point in the same troubling direction as the species&#8217; global trajectory. Preserving natural habitats, the study suggests, is not merely about saving scenic landscapes; it is about safeguarding the genetic library that this cryptic frog, and countless species like it, will need to survive the coming decades of environmental change.</p>
<p><strong>Subject of Research:</strong> Genetic diversity patterns across habitats and morphotypes of the South Asian frog Sphaerotheca maskeyi</p>
<p><strong>Article Title:</strong> Genetic diversity patterns across habitats and forms of a morphologically cryptic South Asian frog (Sphaerotheca maskeyi)</p>
<p><strong>Article References:</strong> Ahmed, W., Amin, H., Rais, M., &amp; DeWoody, J. A. (2026). Genetic diversity patterns across habitats and forms of a morphologically cryptic South Asian frog (Sphaerotheca maskeyi). <em>Molecular Biology Reports, 53</em>(1), Article 1568. <a href="https://doi.org/10.1007/s11033-026-12696-9" rel="noopener noreferrer">https://doi.org/10.1007/s11033-026-12696-9</a></p>
<p><strong>Image Credits:</strong> AI Generated</p>
<p><strong>DOI:</strong> <a href="https://doi.org/10.1007/s11033-026-12696-9" rel="noopener noreferrer">10.1007/s11033-026-12696-9</a></p>
<p><strong>Keywords:</strong> Sphaerotheca maskeyi, genetic diversity, cryptic species, 16S rRNA, RAG-1, phylogenetics, habitat degradation, color polymorphism, AMOVA, amphibian conservation, South Asia, molecular ecology</p>
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