Intraspecific Molecular Diversity Research Articles

Life history and biogeography of the enigmatic mantid Nilomantisfloweri (Mantodea, Nanomantidae).

The biology and distribution patterns of the Sahelian mantid species Nilomantisfloweri are still insufficiently known. For the first time, records are confirmed of this species from Iran and the distribution map of its native range is updated. Records are compiled from the Sahel zone of North Africa, the Arabian Peninsula, and Iran. Detailed information on its biology, oothecal characteristics, male genitalia variation, and intraspecific molecular diversity in the mitochondrial gene cytochrome c oxidase are provided, and ecological niche modelling was used to gain insight into the overall species distribution and understand its climatic niche limits. Genetic analysis revealed only one haplotype shared between Iran and Oman. The Iranian populations likely represent two distinct clusters, both more related to the diverse Oman haplotypes than to each other. Based on new data, N.floweri appears to be mostly associated with coastal areas in southwestern Asia, with the vast majority of records found along the Red Sea, Persian Gulf, and Oman Gulf coasts. This distribution contrasts markedly with N.floweri records in the Sahel, where most collections have been reported in the transitional zone between the southern Sahara and arid thorn savannah, far off the coast. This study contributes to a comprehensive understanding of this still enigmatic mantid species.

Phylogenetic analysis of six different species of Saraca L. (Fabaceae, Caesalpinioideae) based on chloroplast matK gene

Abstract. Sil S, De KK, Ghosh A. 2021. Phylogenetic analysis of six different species of Saraca L. (Fabaceae, Caesalpinioideae) based on chloroplast matK gene. Biodiversitas 22: 3880-3889. Saraca L. is one of the most important genera, with several horticultural and therapeutic values. Specific taxonomic and phylogenetic knowledge of Saraca through molecular data is essential for accessing its true medicinal benefits. Nineteen different Partial matK gene sequences of the chloroplast genome of six different species of Saraca, including four amplified and 15 retrieved from the NCBI gene bank, were place in a sequence alignment. The resulting data were examined to determine their phylogenetic and evolutionary interrelationships. The comparative analysis of different sequences of each of the species revealed intra-specific molecular diversity, and the comparison of the matK sequences of six different species defined their inter-specific molecular diversity. The analysis of partial matK sequences revealed the presence of 87 variable sites, 14 parsimony informative sites, 54 singleton sites, and 237 quadri-fold degenerate sites. The approximate nucleotide composition was A-31.02%, T-37.46%, C-16.06%, and G-15.46%. The value of transition/transversion bias was 0.90. About 522 codons were analyzed and the presence of 34 variable sites, 8 parsimony informative sites, and 25 singleton sites was observed within their respective amino acid sequences. The average pair-wise distance was 0.0444, and 189 segregating sites and 0.018809 nucleotide diversity were observed. The evolution of different species of Saraca and their phylogenetic interrelationships were observed by analyzing their matK sequences. The relative homogeneity of S. indica is quite low. S. dives had the earliest evolutionary trends while S. declinata had the most recent. S. asoca and S. indica are quite similar on the molecular level but can be treated as different species while the difference between S. declinata and one of its synonyms, S. palembanica, indicates the possibility of separating them into different species.

Neither historical climate nor contemporary range fully explain the extant patterns of molecular diversity in marine species

AbstractAimIntraspecific diversity is a significant component of adaptive potential, and thus, it is important to identify the evolutionary processes that have and will continue to shape the molecular diversity of natural populations. This study aims to untangle the possible drivers of intraspecific molecular diversity by testing whether patterns of historical climatic stability or contemporary range position correlate with molecular diversity.LocationSouth African coastline.TaxaThe cape urchin (Parechinus angulosus), common shore crab (Cyclograpsus punctatus) and granular limpet (Scutellastra granularis).MethodsSpecies distributions were hindcasted to the Last Glacial Maximum to assess the biogeography of the study species. Linear models were built to compare the relationships between historical climatic stability or contemporary distributional ranges with extant genetic (mtDNA) and genomic (SNP) diversity.ResultsWe found large differences in the historical ranges among species and time periods. Regions of higher habitat stability corresponded to regions of higher molecular diversity, but historical climatic variability was not a predictor of molecular diversity within linear models. Lower genetic diversity values, and higher genetic differentiation, were detected in edge populations, but this was not consistent across marker type or species.Main conclusionsBoth historical and contemporary processes are potentially driving patterns of diversity, but a large portion of the variation in molecular diversity remains unexplained. Our findings suggest that marine species within cool‐temperate bioregions in the Southern Hemisphere may have more complex biogeographic and evolutionary histories than terrestrial taxa and/or coastal species within northern, formerly glaciated regions.

Substantial differences in genetic diversity and spatial structuring among (cryptic) amphipod species in a mountainous river basin

AbstractRecent advances in molecular methods foster the documentation of small spatial scale biological diversity over large geographical areas. These advances allow to correctly record α‐diversity, but also enable biomonitoring that describes intraspecific molecular diversity, providing valuable insights into the contemporary history of species. Such information is essential for the accurate monitoring of freshwater communities and provides a promising tool to identify conservation priorities at various spatial scales.Here, we combined morphological species determinations with genetic characterisation via DNA barcoding and species distribution modelling. We aimed to investigate whether closely related amphipod species occupying overlapping ecological niches and occurring in partial sympatry, demonstrate similar spatial patterns of intraspecific genetic diversity and share comparable population histories. Therefore, we characterised the amphipod fauna within the Kinzig catchment (1,058 km2, Hesse, Central Germany) that is a tributary of the Main River and part of the long‐term ecological research network using genetics.Our genetic analysis revealed two more taxonomic entities than previously known. The most common species wasGammarus fossarumclade 11 (or type B), followed byGammarus roeseliiclade C,Gammarus pulexclade D,G. pulexclade B and a very rare previously unknown lineage within theG. fossarum‐species complex, which we refer to asG. fossarumclade RMO. These five taxa differed in their intraspecific genetic diversity, withG. fossarumclade 11 demonstrating the highest diversity and having a prominent small‐scale pattern with endemic haplotypes in headwater regions. Distributions were predicted for the three most abundant molecularly identified species.The upstream reaches maintained high intraspecific α‐ and β‐diversity, pointing towards a more complex population structure ofG. fossarumclade 11. This highlights the importance of considering intraspecific diversity for the conservation of individual species. DNA‐based species distribution models shed light on species‐specific habitat preferences, and showed spatial distribution patterns that supported ecological inference and conservation management. Barcoding specimens prior to modelling can increase robustness and performance of distribution models as juveniles can be incorporated, and cryptic species complexes disentangled.Our integrative study contributes to the further development of science‐informed and holistically considered effective conservation measures. Some poorly dispersing hololimnic species may serve as representatives for our understanding of the natural history of the local communities in headwater regions—and their protection. Intraspecific genetic diversity should be considered in conservation management decisions as it can provide valuable information on past and present population demography, connectivity, and recovery processes of species—information that rarely can be achieved by traditional monitoring approaches.

Cryptic diversity of the genus Beauveria with a new species from Thailand

Thailand has rich natural resources and diverse ecosystems. From our surveys of entomopathogenic fungi in Thailand over the last decade, 66 Beauveria strains in BIOTEC Culture Collection (BCC) were studied to account for the diversity of this genus in Thailand. Examination of morphological characteristics from various media and phylogenetic analyses based on partial sequence of ITS, TEF, RBP1, RPB2, and the nuclear intergenic region Bloc, were realized. Among the strains from Thailand, we described here a new species, namely B. mimosiformis sp. nov., isolated from Coleoptera larva in the North of Thailand. This new species has a unique characteristic of phialides and conidia forming an ensemble similar to plant leaves of the genus Mimosa; it has pale yellow to light yellow stromata, cylindrical with rounded apices or oblong conidia, cylindrical part-ascospores. We also found a teleomorph linked to B. asiatica and documented new hosts (Lepidoptera larva and adult beetle) of B. gryllotalpidicola, as well as reported B. malawiensis for the first time in Thailand. Beside those species, B. bassiana and B. loeiensis were also identified, adding up to six species from Thailand. Through molecular phylogenetic analyses, we revealed (1) diverging lineages within B. asiatica and B. bassiana which, despite lack of support to be erected as any higher taxonomical unit, demonstrated complex intra-specific molecular diversity undergoing differentiation and (2) ambiguous relations between certain known species, particularly for B. majiangensis that we synonymized as B. asiatica.

Revisiting the past − novel insight into intraspecific molecular diversity and phylogeny of widespread Echinogammarus berilloni

Echinogammarus berilloni (Catta, 1878) is a widespread and euryecious species, inhabiting large parts of Southwestern Europe. Additionally, it is recognized as one of the non-native and invasive species, increasing its range to Central Europe. Even though it is widely used as a model organism in a variety of ecological and ecotoxicological studies, its intraspecific molecular diversity has been overlooked. In this study, the publicly available genetic data reveal high level of intraspecific diversity, supporting presence of up to four phylogenetically distinct genetic lineages. Furthermore, the results indicate that the taxon is not monophyletic. The importance of considering its intraspecific diversity is discussed, highlighting the potential implications for future studies as well as the need for further detailed taxonomic studies.

Identification of Vietnamese <i>Ochna integerrima</i> (Lour.) Merr Species Based on Ribosomal DNA Internal Transcribed Spacer Sequence

Ochna integerrima is a medicinal and ornamental plant, is widely distributed in Southeast Asia areas. In Vietnam, it has been ranked as the rare and endangered species due to its high demand trade of the beautiful species. In this study, total 21 Ochna samples, collected from the northern and southern areas, were used to characterize the morphological traits using morphological analyses and molecular tool. The results have revealed that the morphological characterization of flower and its quality of Yen Tu Ochna samples showed differences in comparison with the common Ochna and southern Ochna samples. To accurately distinguish genetic traits of the samples, we have sequenced the internal transcribed spacer (ITS) region (including ITS1, 5.8S) of 21 species. The results have disclosed the genetic correlations of the samples ranging from 96.25% to 100% among the studied Ochna samples, of which 5 samples include B1, B2, B3, B6 and N3.1 were divided into the separate groups. The current work is the first report in constructing a molecular database of Ochna for further assessment of inter-and intra-specific molecular diversity of Ochna species in Vietnam.

Identification of Vietnamese <i>Ochna integerrima</i> (Lour.) Merr Species Based on Ribosomal DNA Internal Transcribed Spacer Sequence

Ochna integerrima is a medicinal and ornamental plant, is widely distributed in Southeast Asia areas. In Vietnam, it has been ranked as the rare and endangered species due to its high demand trade of the beautiful species. In this study, total 21 Ochna samples, collected from the northern and southern areas, were used to characterize the morphological traits using morphological analyses and molecular tool. The results have revealed that the morphological characterization of flower and its quality of Yen Tu Ochna samples showed differences in comparison with the common Ochna and southern Ochna samples. To accurately distinguish genetic traits of the samples, we have sequenced the internal transcribed spacer (ITS) region (including ITS1, 5.8S) of 21 species. The results have disclosed the genetic correlations of the samples ranging from 96.25% to 100% among the studied Ochna samples, of which 5 samples include B1, B2, B3, B6 and N3.1 were divided into the separate groups. The current work is the first report in constructing a molecular database of Ochna for further assessment of inter-and intra-specific molecular diversity of Ochna species in Vietnam.

Ancient connections among the European rivers and watersheds revealed from the evolutionary history of the genus Telestes (Actinopterygii; Cypriniformes).

In order to better understand the complex geologic history of the Mediterranean area, we have analysed evolutionary history, phylogeographic structure and molecular diversity of freshwater fishes belonging to the genus Telestes. As primary freshwater fishes distributed largely in the Mediterranean basin, this genus represents a suitable model system for investigating the historical biogeography of freshwater drainage systems in southern Europe. In this investigation we have included samples representing all Telestes species and based our analyses on one mitochondrial and one nuclear gene. We have investigated phylogenetic structure inside the genus Telestes, estimated divergence times, reconstructed ancestral distribution ranges and described intraspecific molecular diversity. Diversification of Telestes started in the Early Miocene, when the ancestors of T. souffia, lineage comprising T. croaticus and T. fontinalis, and the one comprising T. pleurobipunctatus and T. beoticus got isolated. The remaining species are genetically more closely related and form a common cluster in the recovered phylogenetic trees. Complex geological history of southern Europe, including formation of continental bridges, fragmentation of landmass, closing of the sea corridor, local tectonic activities, led to complicated biogeographical pattern of this genus, caused by multiple colonization events and passovers between ancient rivers and water basins. Especially pronounced diversity of Telestes found in the Adriatic watershed in Croatia and Bosnia and Herzegovina is a consequence of a triple colonization of this area by different lineages, which led to an existence of genetically distinct species in neighboring areas. Significant intraspecific structuring is present in T. souffia, T. muticellus, T. croaticus and T. pleurobipunctatus. Besides in well-structured species, elevated levels of genetic polymorphism were found inside T. turskyi and T. ukliva, as a consequence of their old origin and unconstrained evolutionary history.

Towards the Genomic Basis of Local Adaptation in Landraces

Landraces are key elements of agricultural biodiversity that have long been considered a source of useful traits. Their importance goes beyond subsistence agriculture and the essential need to preserve genetic diversity, because landraces are farmer-developed populations that are often adapted to environmental conditions of significance to tackle environmental concerns. It is therefore increasingly important to identify adaptive traits in crop landraces and understand their molecular basis. This knowledge is potentially useful for promoting more sustainable agricultural techniques, reducing the environmental impact of high-input cropping systems, and diminishing the vulnerability of agriculture to global climate change. In this review, we present an overview of the opportunities and limitations offered by landraces’ genomics. We discuss how rapid advances in DNA sequencing techniques, plant phenotyping, and recombinant DNA-based biotechnology encourage both the identification and the validation of the genomic signature of local adaptation in crop landraces. The integration of ‘omics’ sciences, molecular population genetics, and field studies can provide information inaccessible with earlier technological tools. Although empirical knowledge on the genetic and genomic basis of local adaptation is still fragmented, it is predicted that genomic scans for adaptation will unlock an intraspecific molecular diversity that may be different from that of modern varieties.

The genera and species of Comatulidae (Comatulida: Crinoidea): taxonomic revisions and a molecular and morphological guide.

We provide a guide for identification of Comatulidae, a family of crinoid echinoderms, incorporating morphological and molecular evidence. A non-dichotomous key for all genera is included, as well as photographs of species most likely to be encountered in the tropical western Pacific Ocean. Based on sequencing of cytochrome oxidase subunit I (COI), and other genes when necessary, we identified four cases where taxonomic revision was needed. We synonymized Comaster nobilis under Comaster schlegelii, and Clarkcomanthus exilis under Clarkcomanthus comanthipinnus, and re-described Clarkcomanthus albinotus. We also showed the variation of COI sequences within and among species, which varies from lineage to lineage. In some cases, specimens with obvious morphological disparity possessed very little intraspecific molecular diversity (<1%). In others, specimens with nearly identical external appearances exhibited quite divergent COI sequences (up to 6%). These results, combined with the non-dichotomous key herein, offer guidelines for identification and discussion of existing and new species of Comatulidae.

Intraspecific venom variation in the medically significant Southern Pacific Rattlesnake (Crotalus oreganus helleri): Biodiscovery, clinical and evolutionary implications

Due to the extreme variation of venom, which consequently results in drastically variable degrees of neutralization by CroFab antivenom, the management and treatment of envenoming by Crotalus oreganus helleri (the Southern Pacific Rattlesnake), one of the most medically significant snake species in all of North America, has been a clinician's nightmare. This snake has also been the subject of sensational news stories regarding supposed rapid (within the last few decades) evolution of its venom. This research demonstrates for the first time that variable evolutionary selection pressures sculpt the intraspecific molecular diversity of venom components in C. o. helleri. We show that myotoxic β-defensin peptides (aka: crotamines/small basic myotoxic peptides) are secreted in large amounts by all populations. However, the mature toxin-encoding nucleotide regions evolve under the constraints of negative selection, likely as a result of their non-specific mode of action which doesn't enforce them to follow the regime of the classic predator-prey chemical arms race. The hemorrhagic and tissue destroying snake venom metalloproteinases (SVMPs) were secreted in larger amounts by the Catalina Island and Phelan rattlesnake populations, in moderate amounts in the Loma Linda population and in only trace levels by the Idyllwild population. Only the Idyllwild population in the San Jacinto Mountains contained potent presynaptic neurotoxic phospholipase A2 complex characteristic of Mohave Rattlesnake (Crotalus scutulatus) and Neotropical Rattlesnake (Crotalus durissus terrificus). The derived heterodimeric lectin toxins characteristic of viper venoms, which exhibit a diversity of biological activities, including anticoagulation, agonism/antagonism of platelet activation, or procoagulation, appear to have evolved under extremely variable selection pressures. While most lectin α- and β-chains evolved rapidly under the influence of positive Darwinian selection, the β-chain lectin of the Catalina Island population appears to have evolved under the constraint of negative selection. Both lectin chains were conspicuously absent in both the proteomics and transcriptomics of the Idyllwild population. Thus, we not only highlight the tremendous biochemical diversity in C. o. helleri's venom-arsenal, but we also show that they experience remarkably variable strengths of evolutionary selection pressures, within each toxin class among populations and among toxin classes within each population. The mapping of geographical venom variation not only provides additional information regarding venom evolution, but also has direct medical implications by allowing prediction of the clinical effects of rattlesnake bites from different regions. Such information, however, also points to these highly variable venoms as being a rich source of novel toxins which may ultimately prove to be useful in drug design and development. These results have direct implications for the treatment of envenomed patients. The variable venom profile of Crotalus oreganus helleri underscores the biodiscovery potential of novel snake venoms.

Why coelacanths are not ‘living fossils’

A series of recent studies on extant coelacanths has emphasised the slow rate of molecular and morphological evolution in these species. These studies were based on the assumption that a coelacanth is a 'living fossil' that has shown little morphological change since the Devonian, and they proposed a causal link between low molecular evolutionary rate and morphological stasis. Here, we have examined the available molecular and morphological data and show that: (i) low intra-specific molecular diversity does not imply low mutation rate, (ii) studies not showing low substitution rates in coelacanth are often neglected, (iii) the morphological stability of coelacanths is not supported by paleontological evidence. We recall that intra-species levels of molecular diversity, inter-species genome divergence rates and morphological divergence rates are under different constraints and they are not necessarily correlated. Finally, we emphasise that concepts such as 'living fossil', 'basal lineage', or 'primitive extant species' do not make sense from a tree-thinking perspective.

Molecular phylogeny of the endangered Vietnamese Paphiopedilum species based on the internal transcribed spacer of the nuclear ribosomal DNA

We have sequenced the internal transcribed spacer (ITS) region (including ITS1, 5.8S, and ITS2) of 16 species and two varieties of the slipper orchid genus Paphiopedilum in Vietnam. The identification of relationship between those species was also assessed using molecular tool. Most of slipper orchid species in Vietnam are now endangered or threatened to extinction due high demand of ornamental trade of these beautiful species. However, it is difficult to distinguish them without their flowers. Therefore, it is needed to develop molecular markers to accurately identify these species. Our present study is in the view to set the first steps in constructing a molecular database of slipper orchids for future assessment of inter- and intra-specific molecular diversity of Paphiopedilum species from Vietnam, to contribute to the conservation of these valuable orchids. The results showed that highly variable areas (that contain many indels) in ITS region are useful for phylogenetic analysis as the dataset containing these long-indels areas and gave better Jack-knife supports in resolving the relationships of Paphiopedilum species than the modified dataset did.