Population Structure Of Species Research Articles

The Breeding Pattern and Population Genetic Structure of Coptotermes gestroi (Blattodea: Rhinotermitidae) Population in Natural Woodland Habitats

Microsatellite markers are suitable tools for assessing the population structure of eusocial species, especially those with a dynamic breeding system, such as the Asian subterranean termite Coptotermes gestroi (Wasmann) (Blattodea: Rhinotermitidae). Therefore, this study applied seven microsatellite markers to infer the breeding pattern and population genetic structure of C. gestroi found in natural woodland habitats at Universiti Sains Malaysia, Penang, Malaysia. The natural woodland habitat C. gestroi colonies show significant deviation from HWE (all p < 0.05). The uncovered genetic pattern suggested that the C. gestroi colonies presented a combined breeding pattern of mixed- and extended-family colonies with moderate genetic differentiation and elevated inbreeding. In particular, the breeding pattern of C. gestroi colonies was inferred to vary depending on the demographic variation and the age of the colony. Nevertheless, the results revealed comprehensive information on the C. gestroi population structure, habitat-specific to natural woodlands. Furthermore, future studies with exclusive datasets on the population structure of C. gestroi on marginal demography are necessary to enhance the management strategies of this pest species.

Changes in fish resources 5 years after implementation of the 10-year fishing ban in the Chishui River, the first river with a complete fishing ban in the Yangtze River Basin

BackgroundTo rehabilitate the depleted fish resources of the Yangtze River Basin, China, a 10-year fishing ban has been implemented. This national initiative has attracted worldwide attention. The present study aimed to explore the ecological process and recovery effectiveness of this complete fishing ban in the Chishui River, the first river where the fishing ban was enacted in the Yangtze River Basin. Changes in fish resources were analyzed based on investigations conducted 5 years before (2012–2016) and 5 years after (2017–2021) the implementation of the fishing ban in four reaches along the longitudinal gradient.ResultsA total of 140 fish species, including 127 native and 13 exotic species, were collected during the study period. The number of fish species as well as the diversity indices showed no significant temporal changes. However, 11 native species that had disappeared for many years appeared again after the fishing ban. The occurrence rates of some key protected species, Procypris rabaudi, Acipenser dabryanus, Euchiloglanis davidi and Myxocyprinus asiaticus, increased after the fishing ban, while Coreius guichenoti, Percocypris pingi, Onychostoma angustistomata and Leptobotia rubrilabris showed no obvious recovery. The fish assemblage structure in nearly all reaches (except the headwater) showed significant temporal changes with an increase in the relative abundance of larger body-sized species. The population structure of most dominant species improved greatly with the mean standard length and the mean body weight as well as the proportion of larger-sized individuals clearly increasing. In addition, the density of fishes changed dramatically with the catch per unit effort (CPUE) increasing by 140–210% for different study reaches.ConclusionsThe present study confirmed that the complete fishing closure is an effective measure to facilitate fish resources recovery. These results provide valuable references for evaluating the effectiveness of the 10-year fishing ban policy in the entire Yangtze River.

Responses of native freshwater mussels to remediation to remove polychlorinated biphenyl‐contaminated sediments in the upper Hudson River

Abstract The Hudson River, New York, was contaminated with polychlorinated biphenyls (PCBs) from two manufacturing plants over a period of approximately 30 years, and PCBs are still present in sediment and biota today. The river provides habitat for a variety of plants and animals, including native freshwater mussels. A remediation programme, consisting of dredging followed by the placement of backfilled sediment and/or a subaqueous cap, was initiated in 2009 to remove PCB‐contaminated sediments, and managers were concerned about how remediation could affect the mussels. Quantitative surveys were conducted across nine reaches (pools) to estimate species composition, density, population size, population structure, and ecosystem services of mussel assemblages, pre‐ and post‐remediation. Surveys were stratified into remediated areas (targeted for dredging) and non‐remediated areas (not targeted for dredging). Pre‐remediation, the river contained a low diversity, and high, but variable, density of mussels that were strongly dominated by Elliptio complanata. The presence of few fresh dead mussels indicates low natural mortality. Frequent recruitment by many species, varied length classes, and high biomass also support robust assemblages that perform important ecosystem services, such as biofiltration. Remedial activity removed most of the mussels and the associated services that they perform: their density was reduced by 83% and their filtration capacity was reduced by 93%, relative to non‐remediated areas. Areas that were remediated were almost devoid of adult mussels, but the presence of small mussels indicates that natural recolonization is occurring. However, it is unknown whether these assemblages will persist. As mussels are generally long lived and slow growing, natural recovery is anticipated to be slow, in the order of decades.

Age affects otolith shape in a coastal pelagic fish (Scomber colias Gmelin, 1789)

Otolith shape analysis is a common and efficient technique to study the population structure of fish species. This approach compares the overall otolith shape among individuals collected along the species´ distribution range. Otolith shape may change during ontogeny; thus, comparing otolith sample collections comprising multiple and variable age classes may lead to biased results. Therefore, it is crucial to test for possible effects of age on the otolith shape for a given species before interpreting potential differences in otolith collections. Here, we explored the effect of age on the otolith shape of a coastal pelagic fish species with a wide geographical distribution and fast growth rate, the Atlantic chub mackerel Scomber colias (Gmelin, 1789). This effect was tested across different years using different age assignment techniques (direct age reading and age back-calculation) and otolith shape descriptors (Elliptic Fourier and Discrete Wavelet). The results show that the age effect on otolith shape is most noticeable between age-1 and older fish, possibly due to rapid growth during the first year of life. Also, the age effect on otolith shape depended on the descriptor used, being more detected when using the Discrete Wavelet descriptor compared to Elliptic Fourier. Our results highlight the need to carefully examine age effects on otolith shape before conducting population structure analysis on mixed-age sample collections.

Effect of Altitudinal Gradation on Population Structure, Composition and Diversity of Non Timber Forest Product Species of Central Western Ghats of Karnataka

Effect of Altitudinal Gradation on Population Structure, Composition and Diversity of Non Timber Forest Product Species of Central Western Ghats of Karnataka

Genetic variation in Loudetia simplex supports the presence of ancient grasslands in Madagascar

Societal Impact StatementRecognizing Loudetia‐dominated grasslands were widespread prior to human colonization highlights that open ecosystems were and continue to be an important component of Madagascar's biodiversity. A better understanding of the plant species that form grassland ecosystems is necessary for effective land management strategies that support livelihoods, but substantial financial and logistical barriers exist to implementing conservation genetic studies using contemporary genomic tools. Some challenges for population genetic analyses of non‐model polyploids lacking reference genomes can be ameliorated by developing computational resources that leverage a cost‐effective data generation strategy that requires no prior genetic knowledge of the target species. This may benefit conservation programs with small operating budgets while reducing uncertainty compared to status quo microsatellite assays.Summary The extent of Madagascar's grasslands prior to human colonization is unresolved. We used population genetic analyses of a broadly dominant C4 fire‐adapted grass, Loudetia simplex, as a proxy for estimating grassland change through time. We carefully examined the utility of target‐enrichment data for population genetics to make recommendations for conservation genetics. We explored the potential of estimating individual ploidy levels from target‐enrichment data and how assumptions about ploidy could affect analyses. We developed a novel bioinformatic pipeline to estimate ploidy and genotypes from target‐enrichment data. We estimated standard population genetic summary statistics in addition to species trees and population structure. Extended Bayesian skyline plots provided estimates of population size through time for empirical and simulated data. All Malagasy L. simplex individuals sampled in this study formed a clade and possibly indicated an ancestral Central Highland distribution of 800 m in altitude and above. Demographic models suggested grassland expansions occurred prior to the Last Interglacial Period and supported extensive grasslands prior to human colonization. Though there are limitations to target‐enrichment data for population genetic studies, we find that analyses of population structure are reliable. Genetic variation in L. simplex supports widespread grasslands in Madagascar prior to the more recent periods of notable paleoclimatic change. However, the methods explored here could not differentiate between paleoclimatic change near the Last Glacial Maximum and anthropogenic effects. Target‐enrichment data can be a valuable tool for analyses of population structure in the absence a reference genome.

Human-driven degradation impacts on mangroves in southern Sierra Leone

Mangrove ecosystems remove carbon from the atmosphere and store it predominantly in soils constituting an important carbon sink. Additionally, they foster biodiversity and provide ecosystem services supporting local livelihoods and enhancing coastal protection. However, mangroves are declining in extent and experiencing degradation due to human activities as well as climate change impacts like sea-level rise and increasing frequency of extreme events. This study investigated how different levels of human-driven degradation affect forest structure, above- and belowground carbon stocks, tree species composition, and the population structures of dominant tree species. We investigated 19 transects of different degradation levels (pristine, moderately degraded, heavily degraded) in various locations (oceanic, riverine, interior) in the Sherbro river estuary in Sierra Leone.Results showed that total carbon stocks of pristine mangroves amounted to 707 Mg C ha−1 including soils to 1 m depth, which is higher than carbon stocks reported from many other regions in Africa.Degradation resulted in declining basal area, decreasing density of large trees (≥ 30 cm diameter) but increasing stem density of small trees (5–10 cm diameter). All carbon pools declined with increasing degradation across all locations. While above- and belowground carbon decreased by 96 %, soil carbon (up to 1 m depth) decreased by 44 %. Heavy degradation resulted in a change in the dominating species from Rhizophora racemosa to Rhizophora mangle across all locations. Overall, we found major effects of degradation on mangrove characteristics and minor effects of location. We urge conservation of pristine forests, restoration of degraded mangroves, and the establishment of management systems that are ecologically informed and based on a comprehensive understanding of human-driven degradation impacts.

Species Composition and Diversity of Plants along Human-Induced Disturbances in Tropical Moist Sal Forests of Eastern Ghats, India

Plant biodiversity data are prerequisites for the sustainable management of a forest. We used quantitative ecological tools to determine the species composition, diversity (richness and evenness), population structure, distribution patterns, and regeneration status of trees in a Tropical Moist Sal Forest of Eastern Ghats, India. For this purpose, a field inventory was conducted during 2020–2022 in sixteen 1.0 ha forest stands along a human-induced disturbance gradient. A total of 161 species (61 trees, 40 shrubs, 60 herbs) belonging to 77 families and 143 genera were recorded in the 16.0 ha of forest area. The results revealed a significant (p < 0.01) decrease in the tree and shrub species density, basal area, species richness, and diversity along the gradient of disturbance. However, in the case of herbs, the Shannon–Weiner diversity index increased significantly (p < 0.01) with increasing disturbance levels. Irrespective of forest types and disturbance levels, the tree diameter class (10–30 cm) accounted for the highest stem density in the forest. A mixed trend was found in the case of the basal area; the >41 cm diameter class constituted the highest basal area in the Pure Sal Forest while the 10–30 cm class was in the Moist Deciduous Forest without Sal. Tree species richness was found higher in lower diameter classes. Disturbances impacted the distribution pattern of trees; in the Pure Sal Forest, the contagious distribution of trees were 61.54%, 40%, and 12.5% in undisturbed, low-disturbed, and moderately disturbed sites, respectively. The percent of trees showing random and regular distribution increased with the increased level of disturbance in all forest types. The number of tree species having good regeneration decreased with the increased disturbance intensity in all forest types. Frequent grazing, repeated forest fires, and poor soil seed banks at the Moderately Disturbed site were the main reasons for the poor/no regeneration of Pterocarpus marsupium, Adina cordifolia, Terminalia bellerica, and some other economical species. Significant changes in structural attributes of the tree community revealed the impact of human-induced disturbances in the Moist Sal Forests of Eastern Ghats. The disturbance mosaics promoted the growth of many invasive weed species and lianas, depleting the number of valuable species in the forest. This study suggests the adaption of sustainable biodiversity conservation approaches through the active participation of the tribal so that the remnants the Moist Sal Forests of Eastern Ghats can be controlled to prevent further degradation.

Environmental DNA reveals the genetic diversity and population structure of an invasive species in the Laurentian Great Lakes

Environmental DNA (eDNA) has been established as a noninvasive and efficient approach to sample genetic material from aquatic environments. Although most commonly used to determine species presence and measure biodiversity, eDNA approaches also hold great potential to obtain population-level genetic information from water samples. In this study, we sequenced a panel of multiallelic microsatellite markers from filtered water and fish tissue samples to uncover patterns of intraspecific diversity in the freshwater Round Goby (Neogobius melanostomus) across their invaded range in the Laurentian Great Lakes region. Although we found that the concentration of nuclear eDNA is lower than mitochondrial eDNA, we nonetheless detected over two-thirds of all nuclear alleles identified from genotyped tissues in our eDNA samples, with the greatest recovery of common alleles in the population. Estimates of allele frequencies and genetic variability within and between populations were detected from eDNA in patterns that were consistent with individual tissue-based estimates of genetic diversity and differentiation. The strongest genetic differentiation in both eDNA and tissues exists in an isolation by distance pattern. Our study demonstrates the potential for eDNA-based approaches to characterize key population parameters required to effectively monitor, manage, or sustain aquatic species.

Conservation genetics of endangered Trillium govanianum Wall. ex D. Don – A pharmaceutically prized medicinal plant from the Himalaya and implications for species recovery

Understanding the genetic diversity and population structure of pharmaceutically important endangered plant species is crucial for their conservation and sustainable use. Despite the continuous population decline in Trillium govanianum Wall. ex D. Don, a highly prized medicinal plant endemic to the Himalaya, information regarding its conservation genetics has been lacking. Here, we employed a conservation genetics approach to investigate how drastically declining populations in natural habitats impact population genetic diversity and structure of this endangered species across the Kashmir Himalaya. We used Start codon targeted (SCoT) and Simple sequence repeat (SSR) markers to assess the intra- and inter-population genetic variation in seven sites across the study region. Based on these markers, we found a very low genetic diversity in T. govanianum populations. Very low levels of observed heterozygosity (Ho = 0.000) and that expected (He = 0.064) in the populations indicate high heterozygote deficiency and high levels of inbreeding depression (FIS = 1.000). A high genetic differentiation was observed among the populations for both SCoT (Gst = 0.719) and SSR (Fst = 0.707) markers. Both the markers showed low gene flow, SCoT (Nm = 0.195) and SSR (Nm = 0.119), depicting high among-population variation than within-population variation. Analysis of molecular variance also indicated a higher genetic variation between the populations than within populations. We also observed a significant positive correlation between genetic divergence and geographical distance, indicating that genetic differentiation in T. govanianum follows a pattern of isolation by distance. Bayesian structure and cluster analysis grouped the populations according to their geographical proximity. Further, redundancy analysis (RDA) revealed the presence of one polymorphic locus for each marker with high discriminatory power. Overall, our findings reveal a very low genetic diversity, high levels of inbreeding, and high genetic differentiation among the populations; likely resulting from habitat fragmentation, population isolation, bottleneck effect, low gene flow, and predominantly asexual reproduction currently operative in the species. Finally, based on the insights gained, we discuss the potential implications of our findings in guiding species recovery and habitat rehabilitation of T. govanianum in the Himalaya with conservation lessons for elsewhere in the world.

Integrative Analysis of Retusa pertenuis (Heterobranchia: Cephalaspidea) from Arctic and Russian Far East Seas with Discussion of Its Morphology, Validity and Population Structure

Retusa pertenuis is still formally considered a junior subjective synonym of Retusa obtusa, despite previous data indicating R. pertenuis and R. obtusa differ significantly in copulatory system morphology. In this paper, we study the species identity and population structure of R. pertenuis with an integrative approach combining morphological and molecular data. The external morphology, head copulatory system and gizzard plates were studied using light microscopy and scanning electron microscopy. We also obtained two mitochondrial (COI and 16S) and two nuclear (H3 and 28S) markers to test the monophyly of R. pertenuis and R. obtusa. Populations from the White Sea, Sea of Okhotsk and Sea of Japan were studied using COI and 18S molecular markers. Our results show that Retusa obtusa sensu lato represents a species complex of at least four species: the nominative species occurring in the North Atlantic, the widely distributed R. pertenuis and two additional species whose identities should be clarified in further studies. Retusa pertenuis geographic range encompasses the North Atlantic, Eurasia’s northern seas, the Canadian Arctic, the Bering Sea, the Sea of Okhotsk and the Sea of Japan. Within R. pertenuis’s range, this species demonstrates a wide variability in shell morphology.

Matching an Old Marine Paradigm: Limitless Connectivity in a Deep-Water Fish over a Large Distance.

Investigations of population structuring in wild species are fundamental to complete the bigger picture defining their ecological and biological roles in the marine realm, to estimate their recovery capacity triggered by human disturbance and implement more efficient management strategies for fishery resources. The Blackspot Seabream (Pagellus bogaraveo, Brünnich 1768) is a commercially valuable deep-water fish highly exploited over past decades. Considering its exploitation status, deepening the knowledge of intraspecific variability, genetic diversity, and differentiation using high-performing molecular markers is considered an important step for a more effective stock assessment and fishery management. With one of the largest efforts conceived of and completed by countries overlooking the Atlantic and Mediterranean coasts in recent years, a total of 320 individuals were collected from different fishing grounds in the Mediterranean Sea and Atlantic Ocean and analysed using 29 microsatellite loci. We applied multiple statistical approaches to investigate the species' connectivity and population structure across most of its described distribution area. Considering the incomplete knowledge regarding the migratory behaviour of adults, here we suggest the importance of egg and larval dispersal in sustaining the observed genetic connectivity on such a large geographical scale.

Genetic Diversity and Population Structure of Juniperus seravschanica Kom. Collected in Central Asia.

Juniperus seravschanica Kom. is a species that grows widely in the mountain ranges from Central Asia to Oman. It is an important tree for the formation of shrub-forest massifs in mountainous areas and for draining and fixing soils from middle to high altitudes. A comprehensive study of the species' genetic diversity and population structure is a basic approach to understanding the current status of J. seravschanica resources for the development of future conservation strategies. Samples from 15 populations of J. seravschanica were collected from the mountain ranges of Uzbekistan, Kyrgyzstan, and Kazakhstan. The genetic diversity and population structure of 15 Central Asian populations of J. seravschanica were assessed using 11 polymorphic simple sequence repeat (SSR) markers. Genetic diversity parameters, including the number of alleles (na), the effective number of alleles (ne), Shannon's information index (I), the percentage of polymorphic loci (PPL), Nei's genetic diversity index (Nei), principal coordinate analysis (PCoA), etc., were evaluated. The analysis of 15 J. seravschanica populations based on 11 polymorphic SSRs detected 35 alleles. The average PIC value was 0.432, and the highest value (0.662) was found in the JT_40 marker. Nei's genetic diversity index for the J. seravschanica populations was 0.450, ranging from 0.407 (population 14) to 0.566 (population 4). The analysis of molecular variance (AMOVA) showed that 90.3% of total genetic variation is distributed within the population. Using the alleles of all the populations, the gene flow (Nm) was found to be 4.654. Population structure analysis revealed poor clustering in the studied populations and confirmed our AMOVA results. The output of this work can be efficiently used for the maintenance of the species across the Central Asian region.

Molecular phylogeny of plant pathogenic fungi based on start codon targeted (SCoT) polymorphism.

A number of molecular marker systems have been developed to assess genetic diversity, carry out phylogenetic analysis, and diagnose and discriminate plant pathogenic fungi. The start codon targeted (SCoT) markers system is a novel approach used here to investigate intra and interspecific polymorphisms of phytopathogenic fungi. This study assessed genetic variability between and within 96 isolates of ten fungal species associated with a variety of plant species using 36 SCoT primers. The six primers generated 331 distinct and reproducible banding patterns, of which 322 were polymorphic (97.28%), resulting in 53.67 polymorphic bands per primer. All primers produced informative amplification profiles that distinguished all fungal species. With a resolving power of 10.65, SCoT primer 12 showed the highest polymorphism among species, followed by primer 33 and primer 29. Polymorphic loci (PPL), Nei's diversity index (h), and Shannon index (I) percentages were 6.25, 0.018, and 0.028, respectively. UPGMA analysis separated all isolates based on morphological classification and revealed significant genetic variation among fungal isolates at the intraspecific level. PCoA analysis strongly supported fungal species discrimination and genetic variation. The other parameters of evaluation proved that SCoT markers are at least as effective as other DNA markers. SCoT markers were effective in identifying plant pathogenic fungi and were a powerful tool for estimating genetic variation and population structure of different fungi species.

Classification of birdsong spectrograms based on DR-ACGAN and dynamic convolution

Birdsongs are highly valuable for bird studies as they provide insights into various aspects such as species distribution, population structures, and habitat. Recognizing birdsongs plays a crucial role in bird conservation efforts. However, manually collecting a large number of birdsongs from the natural environment is expensive and time-consuming. Moreover, using limited birdsong data often results in low classification accuracy of the models. To better identification of birdsongs, we utilize wavelet transform(WT) to convert them into spectrograms, which contain abundant energy and frequency information. Effectively extracting these features is vital to improve the classification accuracy of the model. To address this problem, we proposed an improved ACGAN model based on residual structure and attention mechanism named DR-ACGAN, which achieved stable training of the model and high-quality generated birdsong spectrograms. The dynamic convolution kernel is then fused with MobileNetV2, ResNet18, and VGG16 models and trained on different datasets, which used different ways of mixing the generated and original spectrograms. The experimental results show that the classification accuracy after data augmentation improves by 6.66%, 4.35%, and 2.29% compared to the original dataset in the three base classifiers. After adding dynamic convolutional kernel structure, the accuracy is further improved by 1.68%, 0.67%, and 0.38% on average which the VGG16 model achieves the highest accuracy of 97.60%.

Seasonal Changes in Vertical Distribution and Population Structure of the Dominant Hydrozoan Aglantha digitale in the Western Subarctic Pacific

Hydrozoans are numerically dominant taxa in gelatinous zooplankton communities of the worldwide oceans and play an energy transfer role connecting primary producers and higher trophic level organisms. In the western subarctic Pacific, St. K2 has been established as a long-term time-series monitoring station. Various studies on zooplankton have been conducted, while hydrozoans have not been treated. This study presents the abundance, vertical distribution, and population structure of the dominant hydrozoan species (Aglantha digitale) at St. K2. Samples collected by vertical stratification samplings from eight layers of 0–1000 m both day and night during four seasons in one year. Hydrozoans occur throughout the year. The annual mean abundance of A. digitale was 198.4 ind. m−2 and composed of 91.9% of hydrozoans. The vertical distribution of A. digitale was concentrated for the epipelagic layer (0–200 m), both day and night of the most season. The bell height (BH) of A. digitale ranged between 2.4–18.9 mm. Most of the mature individuals, with gonad length larger than 10% of BH, occurred only in July. The BH of mature individuals ranged from 4.7 to 17.6 mm, with the BH of most mature individuals were larger than >10 mm. Through observation on BH at each sampling layer, small individuals with BH < 6 mm were distributed below 300 m depths throughout the seasons, expanding their vertical distribution to the deeper layers. Inter-region comparison of abundance, maturation body size, and generation length of A. digitale revealed that these parameters are varied with the region and depend on the marine ecosystem structures.

Population genetic structure of the bentfin devil ray (Mobula thurstoni) in the South Indonesia Sea with limited sample based on ND5 gene

Abstract. Wardana ED, Putra ING, Al Malik MD, Yusmalinda NLA, Ningsih EY, Pertiwi NPD, Salim MG, Kanedi MM, Putra MIH, Sembiring A. 2023. Population genetic structure of the bentfin devil ray (Mobula thurstoni) in the South Indonesia Sea with limited sample based on ND5 gene. Biodiversitas 24: 3743-3749. Bentfin devil ray (Mobula thurstoni) is one of five Mobula rays with a worldwide distribution. This species has high economic value and play an essential ecological role. However, due to their biological characteristics, such as low reproductive rates and late maturity, these species are highly vulnerable to overfishing and slow to recover from depletion. Genetic information, such as this species's population structure and genetic diversity is limited. This study aimed to determine the genetic variation and population structure of M. thurstoni in the South Indonesia Sea based on mitochondrial DNA from ND5 gene. Twenty-two samples of M. thurstoni were successfully collected from three locations Palabuhanratu (n=5), Muncar (n=13), and Savu Sea (n= 4). The haplotype diversity (Hd) ranged from 0.782 to 1.00 (mean=0.839), and Nucleotide diversity (?) ranged from 0.004 to 0.018 (mean=0.007). Then, no significant population differences (P-value > 0.05) were observed between locations, indicating that M. thurstoni population in the South Indonesian Sea represents a single genetic population. Additionally, the haplotype distribution also indicated the presence of two shared haplotypes between locations. Consequently, co-management strategies for sustainable fishing and conservation must be implemented across these three locations to ensure the sustainability of this species in the nature habitat.

Morphology and Mitochondrial Lineage Investigations Corroborate the Systematic Status and Pliocene Colonization of Suncus niger (Mammalia: Eulipotyphla) in the Western Ghats Biodiversity Hotspot of India.

The Indian highland shrew, Suncus niger (Horsfield, 1851), is the least studied soricid species from its original range distribution in Southern India, with several systematics conundrums. Following its discovery in 1851, the species was synonymized with Suncus montanus (Kelaart, 1850) (endemic to Sri Lanka) and subsequently identified as a separate Indian population. However, the systematic status of S. niger from topotype specimens in Southern India has yet to be determined through an integrated approach. Both taxonomy and mitochondrial genetic data (Cytochrome b and 16S ribosomal RNA) were used to re-examine the systematics of S. niger. The mtCytb gene clearly distinguished topotypic S. niger from other Suncus species, with high genetic divergences varying from 8.49% to 26.29%. Further, the Bayesian and maximum likelihood topologies clearly segregated S. niger from other congeners and corroborated the sister relationship with S. stoliczkanus with expected divergence in the late Pliocene (2.62 MYA). The TimeTree analysis also exhibits a strong matrilineal affinity of S. dayi (endemic to India) toward the African species. The current study hypothesizes that the ancestor of the soricids evolved in Africa and that genetic lineages were subsequently shifted by plate tectonic events that subsequently colonized different continents as distinct species during the late Miocene (Tortonian) to the Holocene era. In addition to the new range expansion and elevation records of S. niger in the Central Western Ghats, we propose that additional sampling across its distribution, as well as the use of multiple genetic markers, may be useful in determining the genetic diversity and population structure of this endemic species. The present study also recommends that more molecular data on the Soricomorphs lineages, and estimates of their divergence times, will shed light on the evolution of these small mammals on Earth.

Genome assembly and resequencing analyses provide new insights into the evolution, domestication and ornamental traits of crape myrtle.

Crape myrtle (Lagerstroemia indica) is a globally used ornamental woody plant and is the representative species of Lagerstroemia. However, studies on the evolution and genomic breeding of L. indica have been hindered by the lack of a reference genome. Here we assembled the first high-quality genome of L. indica using PacBio combined with Hi-C scaffolding to anchor the 329.14-Mb genome assembly into 24 pseudochromosomes. We detected a previously undescribed independent whole-genome triplication event occurring 35.5 million years ago in L. indica following its divergence from Punica granatum. After resequencing 73 accessions of Lagerstroemia, the main parents of modern crape myrtle cultivars were found to be L. indica and L. fauriei. During the process of domestication, genetic diversity tended to decrease in many plants, but this was not observed in L. indica. We constructed a high-density genetic linkage map with an average map distance of 0.33cM. Furthermore, we integrated the results of quantitative trait locus (QTL) using genetic mapping and bulk segregant analysis (BSA), revealing that the major-effect interval controlling internode length (IL) is located on chr1, which contains CDL15, CRG98, and GID1b1 associated with the phytohormone pathways. Analysis of gene expression of the red, purple, and white flower-colour flavonoid pathways revealed that differential expression of multiple genes determined the flower colour of L. indica, with white flowers having the lowest gene expression. In addition, BSA of purple- and green-leaved individuals of populations of L. indica was performed, and the leaf colour loci were mapped to chr12 and chr17. Within these intervals, we identified MYB35, NCED, and KAS1. Our genome assembly provided a foundation for investigating the evolution, population structure, and differentiation of Myrtaceae species and accelerating the molecular breeding of L. indica.

Clonality, local population structure and gametophyte sex ratios in cryptic species of the Sphagnum magellanicum complex.

Sphagnum (peatmoss) comprises a moss (Bryophyta) clade with ~300-500 species. The genus has unparalleled ecological importance because Sphagnum-dominated peatlands store almost a third of the terrestrial carbon pool and peatmosses engineer the formation and microtopography of peatlands. Genomic resources for Sphagnum are being actively expanded, but many aspects of their biology are still poorly known. Among these are the degree to which Sphagnum species reproduce asexually, and the relative frequencies of male and female gametophytes in these haploid-dominant plants. We assess clonality and gametophyte sex ratios and test hypotheses about the local-scale distribution of clones and sexes in four North American species of the S. magellanicum complex. These four species are difficult to distinguish morphologically and are very closely related. We also assess microbial communities associated with Sphagnum host plant clones and sexes at two sites. Four hundred and five samples of the four species, representing 57 populations, were subjected to restriction site-associated DNA sequencing (RADseq). Analyses of population structure and clonality based on the molecular data utilized both phylogenetic and phenetic approaches. Multi-locus genotypes (genets) were identified using the RADseq data. Sexes of sampled ramets were determined using a molecular approach that utilized coverage of loci on the sex chromosomes after the method was validated using a sample of plants that expressed sex phenotypically. Sex ratios were estimated for each species, and populations within species. Difference in fitness between genets was estimated as the numbers of ramets each genet comprised. Degrees of clonality [numbers of genets/numbers of ramets (samples)] within species, among sites, and between gametophyte sexes were estimated. Sex ratios were estimated for each species, and populations within species. Sphagnum-associated microbial communities were assessed at two sites in relation to Sphagnum clonality and sex. All four species appear to engage in a mixture of sexual and asexual (clonal) reproduction. A single ramet represents most genets but two to eight ramets were dsumbers ansd text etected for some genets. Only one genet is represented by ramets in multiple populations; all other genets are restricted to a single population. Within populations ramets of individual genets are spatially clustered, suggesting limited dispersal even within peatlands. Sex ratios are male-biased in S. diabolicum but female-biased in the other three species, although significantly so only in S. divinum. Neither species nor males/females differ in levels of clonal propagation. At St Regis Lake (NY) and Franklin Bog (VT), microbial community composition is strongly differentiated between the sites, but differences between species, genets and sexes were not detected. Within S. divinum, however, female gametophytes harboured two to three times the number of microbial taxa as males. These four Sphagnum species all exhibit similar reproductive patterns that result from a mixture of sexual and asexual reproduction. The spatial patterns of clonally replicated ramets of genets suggest that these species fall between the so-called phalanx patterns, where genets abut one another but do not extensively mix because of limited ramet fragmentation, and the guerrilla patterns, where extensive genet fragmentation and dispersal result in greater mixing of different genets. Although sex ratios in bryophytes are most often female-biased, both male and female biases occur in this complex of closely related species. The association of far greater microbial diversity for female gametophytes in S. divinum, which has a female-biased sex ratio, suggests additional research to determine if levels of microbial diversity are consistently correlated with differing patterns of sex ratio biases.