Greater Genetic Differentiation Research Articles

Analysis of the Mitochondrial COI Gene and Genetic Diversity of Endangered Goose Breeds.

The mitochondrial cytochrome c oxidase subunit I (COI) genes of six endangered goose breeds (Xupu, Yangjiang, Yan, Wuzong, Baizi, and Lingxian) were sequenced and compared to assess the genetic diversity of endangered goose breeds. By constructing phylogenetic trees and evolutionary maps of genetic relationships, the affinities and degrees of genetic variations among the six different breeds were revealed. A total of 92 polymorphic sites were detected in the 741 bp sequence of the mtDNA COI gene after shear correction, and the GC content of the processed sequence (51.11%) was higher than that of the AT content (48.89%). The polymorphic loci within the populations of five of the six breeds (Xupu, Yangjiang, Yan, Baizi, and Lingxian) were more than 10, the haplotype diversity > 0.5, and the nucleotide diversity (Pi) > 0.005, with the Baizi geese being the exception. A total of 35 haplotypes were detected based on nucleotide variation among sequences, and the goose breed haplotypes showed a central star-shaped dispersion; the FST values were -0.03781 to 0.02645, The greatest genetic differentiation (FST = 0.02645) was observed in Yan and Wuzong breeds. The most frequent genetic exchange (Nm > 15.00) was between the Wuzong and Yangjiang geese. An analysis of molecular variance showed that the population genetic variation mainly came from within the population; the base mismatch differential distribution analysis of the goose breeds and the Tajima's D and Fu's Fs neutral detection of the historical occurrence dynamics of their populations were negative (p > 0.10). The distribution curve of the base mismatches showed a multimodal peak, which indicated that the population tended to be stabilised. These results provide important genetic information for the conservation and management of endangered goose breeds and a scientific basis for the development of effective conservation strategies.

Comparative mitochondrial genome analysis provides new insights into the classification of Modiolinae.

Mitochondrial genomes have become a powerful tool for studying molecular genetics and phylogeny of mollusks. Currently, the position of Modiolinae within Mytilidae and the taxonomic and phylogenetic relationships within Modiolinae were still controversial. This study focuses on the complete mitochondrial genomes of two species: Modiolus modulaides (Röding, 1798) and Modiolus auriculatus Krauss, 1848, which have not been sequenced before. We assembled and characterized the mitochondrial genomes of M. modulaides and M. auriculatus and then analyzed the phylogenetic relationships. The mitochondrial genomes of M. modulaides and M. auriculatus were 15,422bp and 16,027bp, respectively. Both of them were composed of 36 functional genes, including 12 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs. All protein-coding genes showed A + T bias, positive GC skews, and negative AT skews in nucleotide composition. Phylogenetic analysis based on the mitochondrial genomes showed that Modiolinae and Bathymodiolinae clustered together to form a sister relationship. Seven Modiolinae species were divided into two clades: L1 (M. modulaides, M. auriculatus and Modiolus philippinarum Hanley, 1843) and L2 [Modiolus modiolus (Linnaeus, 1758), Modiolus kurilensis Bernard, 1983, Modiolus nipponicus (Oyama, 1950), and Modiolus comptus (Sowerby III, 1915)]. The divergence time of the two clades was approximately 105.75Ma. Furthermore, the transfer RNA gene rearrangement, longer genetic distance, and greater genetic differentiation were confirmed between the L1 and L2 clades, as well as differences in the external characteristics of the shells of the two clades. Based on the molecular data, it was speculated that species from the L1 clade might belong to other genera or new genera. This study provides molecular information for further taxonomic and phylogenetic studies of Mytilidae.

Adaptive Evolution of Two Distinct Adaptive Haplotypes of Neanderthal Origin at the Immunoglobulin Heavy-chain Locus in East Asian and European Populations.

Immunoglobulins (Igs) have a crucial role in humoral immunity. Two recent studies have reported a high-frequency Neanderthal-introgressed haplotype throughout Eurasia and a high-frequency Neanderthal-introgressed haplotype specific to southern East Asia at the immunoglobulin heavy-chain (IGH) gene locus on chromosome 14q32.33. Surprisingly, we found the previously reported high-frequency Neanderthal-introgressed haplotype does not exist throughout Eurasia. Instead, our study identified two distinct high-frequency haplotypes of putative Neanderthal origin in East Asia and Europe, although they shared introgressed alleles. Notably, the alleles of putative Neanderthal origin reduced the expression of IGHG1 and increased the expression of IGHG2 and IGHG3 in various tissues. These putatively introgressed alleles also affected the production of IgG1 upon antigen stimulation and increased the risk of systemic lupus erythematosus. Additionally, the greatest genetic differentiation across the whole genome between southern and northern East Asians was observed for the East Asian haplotype of putative Neanderthal origin. The frequency decreased from southern to northern East Asia and correlated positively with the genome-wide proportion of southern East Asian ancestry, indicating that this putative positive selection likely occurred in the common ancestor of southern East Asian populations before the admixture with northern East Asian populations.

Genetic diversity and phylogeographic patterns of the peacock jewel-damselfly, Rhinocypha fenestrella (Rambur, 1842).

Despite is known to have widespread distribution and the most active species of the family Chlorocyphidae, the molecular data of Rhinocypha fenestrella (Rambur, 1842) are relatively scarce. The present study is the first that examined the genetic diversity and phylogeographic pattern of the peacock jewel-damselfly R. fenestrella by sequencing the cytochrome C oxidase I (cox1) and 16S rRNA gene regions from 147 individuals representing eight populations in Malaysia. A total of 26 and 10 unique haplotypes were revealed by the cox1 and 16S rRNA genes, respectively, and 32 haplotypes were recovered by the concatenated sequences of cox1+16S. Analyses indicated that haplotype AB2 was the most frequent and the most widespread haplotype in Malaysia while haplotype AB1 was suggested as the common ancestor haplotype of the R. fenestrella that may arose from the Negeri Sembilan as discovered from cox1+16S haplotype network analysis. Overall haplotype and nucleotide diversities of the concatenated sequences were Hd = 0.8937 and Pi = 0.0028, respectively, with great genetic differentiation (FST = 0.6387) and low gene flow (Nm = 0.14). Population from Pahang presented the highest genetic diversity (Hd = 0.8889, Pi = 0.0022, Nh = 9), whereas Kedah population demonstrated the lowest diversity (Hd = 0.2842, Pi = 0.0003, Nh = 4). The concatenated sequences of cox1+16S showed genetic divergence ranging from 0.09% to 0.97%, whereas the genetic divergence for cox1 and 16S rRNA genes were 0.16% to 1.63% and 0.01% to 0.75% respectively. This study provides for the first-time insights on the intraspecific genetic diversity, phylogeographic pattern and ancestral haplotype of Rhinocypha fenestrella. The understanding of molecular data especially phylogeographic pattern can enhance the knowledge about insect origin, their diversity, and capability to disperse in particular environments.

Genetic structure of ten Artemia populations from China: cumulative effects of ancient geological events, climatic changes, and human activities

This study investigated the population genetics and distribution patterns of Artemia populations from ten inland salt lakes in China. A total of 1,274,698 Artemia single nucleotide polymorphisms (SNPs) were identified. The results showed that these populations could be geographically and genetically divided into four distinct groups, and that the Tibetan populations were further divided into two subpopulations with a trend of decreasing genetic diversity from west to east. The Tibetan population had the highest genetic diversity, whereas the Shanxi population had the lowest. There was moderate genetic differentiation between the Tibetan populations and greater genetic differentiation between the Xinjiang and Shanxi populations. IBD (isolation by distance) suggested that geographical isolation contributes to genetic differentiation. In addition, there was some degree of gene flow among the ten populations, with A. sinica showing unidirectional gene flow in all populations in the eastern Nagri region. Species distribution modeling showed that mean annual temperature, temperature seasonality, and annual precipitation were the main environmental factors affecting the distribution of Artemia populations and suitable habitats for Tibetan populations will be further reduced in the future. It is necessary to strengthen the protection of germplasm resources and formulate scientific protocols for the sustainable development and utilization of Artemia resources.

Genomic diversity and population structure of teosinte (Zea spp.) and its conservation implications.

The wild species of the genus Zea commonly named teosintes, comprise nine different taxa, distributed from northern Mexico to Costa Rica. Although this genus of plants has been extensively studied from a morphological, ecogeographical and genetic point of view, most contributions have been limited to the study of a few populations and taxa. To understand the great variability that exists between and within teosinte species, it is necessary to include the vast majority of known populations. In this context, the objective of this work was to evaluate the diversity and genomic structure of 276 teosinte populations. Molecular analyzes were performed with 3,604 plants and with data from 33,929 SNPs. The levels of genetic diversity by taxonomic group show a marked difference between species, races and sections, where the highest values of genomic diversity was found in ssp. parviglumis and ssp. mexicana. The lower values were obtained for the Luxuriantes section as well as ssp. huehuetenagensis of the section Zea. The results of structure show that there is a great genetic differentiation in all the taxonomic groups considered. For ssp. parviglumis and mexicana, which are the taxa with the largest number of populations, a marked genomic differentiation was found that is consistent with their geographic distribution patterns. These results showed a loss of diversity in several teosinte populations, making a strong case for further collection, and ex situ and in situ conservation. Also, this study highlights the importance of integrating genomic diversity and structure for the applications of conservation and management.

Population structure and mixed reproductive strategies in Bipolaris maydis from single and multiple corn cultivars in Fujian Province, China.

Bipolaris maydis is the pathogenic microorganism of southern corn leaf blight, a persistent biotic constraint responsible for substantial yield losses of corn worldwide. In the present study, 96 isolates from six representative fields growing single and multiple sweet corn cultivars in Pingnan, Fuqing, and Jian'ou in Fujian Province, which are characterized by different geographical characteristics and cropping patterns, were genetically analyzed using inter-simple sequence repeat (ISSR) markers to assess the impact of geographical origins and corn cultivars on B. maydis population differentiation. B. maydis isolates originated from diverse regions possessed higher genetic variety than those from single and multiple sweet corn cultivars. Phylogenetic analysis showed that the isolates from single and multiple sweet corn cultivars were randomly grouped into different clusters, with those from the same location tending to form clusters. A greater genetic differentiation among different geographical populations than between those from single and multiple sweet corn cultivars was observed by pairwise comparison. Hierarchical analysis indicated that among-population variation was higher when comparatively analyzed B. maydis populations from different locations than in those from single and multiple sweet corn cultivars. In conclusion, these results suggest that geographical origin acts a more considerable role in genetic differentiation of B. maydis than corn cultivar. Two divided genetic clusters were detected in the B. maydis populations from single and multiple sweet corn cultivars at the three locations in Fujian Province, with major genetic variation being derived within populations. The high haplotypic diversity and expected mating type ratio of 1:1 in combination with significant linkage disequilibrium suggested that a mixed reproductive strategy occurs in the B. maydis population in Fujian Province. This study will enrich the information on the role that geographical origins and corn cultivars play in the population structure of the pathogen as well as the reproductive strategies in B. maydis population in Fujian Province.

Body color selection of domesticated carp (Cyprinus carpio) in traditional agricultural systems: Insight provided by growth performance, nutritional quality, and genetic diversity

The body color retention of domesticated organisms in traditional agricultural systems results from long-term natural selection and human intervention, which usually encompasses the local understanding and management experience of the species. Exploiting the body color trait advantage and genetic potential of domesticated animals will help to select breeding stock, improve farmers' economic income, and provide insight into future sustainable agriculture design to utilize locally appropriate populations. In this study, the rice-fish coculture system, a Global Important Agriculture Heritage System (GIAHS) in Qingtian County, Zhejiang Province, China, was selected as the representative research system. Four body color (red, red-black, bronze and cyan) of the indigenous species Qingtian paddy field carp (Cyprinus carpio) were selected to compare the economic trait advantages such as the growth performance, nutritional quality of the fish, and the rice yield cocultured with the carp. Besides, the genetic resources and population structure of different body colors were also examined through mitochondrial D-loop gene. Our results show that there are two subgroups of the four populations (K = 2). Among them, the bronze-colored group occupied one subgroup with a large number of unique haplotypes, showing great genetic differentiation from other body color groups. The red and the red-black-colored groups have higher genetic diversity and more frequent gene flow between each other. The genetic diversity of the cyan and the bronze-colored groups were relatively low with more regionally restricted. Three economic indexes showed that the nutritive values of the carps with the four body colors were relatively similar and had no effect on rice yield under the same feeding conditions. Among them, the red-black-colored group had the best specific growth rate (SGR, P < 0.01), weight gain rate (WGR, P < 0.01) and linoleic acid content (P < 0.05). The cyan-colored group had the lowest WGR and SGR, but had the strongest paddy field survival ability (P < 0.01). In summary, the red-black-colored group are rich in genetic diversity and have the best breeding potential and environmental adaptability, which is the most suitable body color for paddy field cultivation.

Population Structure and Genetic Diversity of Colletotrichum gloeosporioides on Citrus in China

To analyze the genetic structure and genetic diversity of Colletotrichum gloeosporioides as the dominant Colletotrichum species on Citrus, the Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genetic diversity, including 63 strains isolated and selected from 8 different sites and 5 different citrus species, was studied. A total of 19 GAPDH haplotypes were identified by genetic analysis, and the main haplotype (haplotype 5) was distributed in 28 isolates, mainly from Citrus unchiu Hort. ex Tanaka (WG) and Citrus reticulata Blanco cv. Succosa (BDZ) in Huangyan (HY), Linhai (LH), and Jiande (JD) of Zhejiang province, and Mashui tangerine (MSJ) in Mengshan of Guangxi province (GX). Using the genetic differentiation index, Fst revealed significant genetic differentiation in C. gloeosporioides populations between Jiangxi province (JXGZ) and GX, HY, LH, JD, and Chun’an (CA) of Zhejiang province, and also revealed slightly less genetic differentiation for C. gloeosporioides populations between HY, LH, JD, GX, Shaanxi province (SX), and Quzhou (QZ) of Zhejiang province. In addition, Fst revealed great genetic differentiation between the C. gloeosporioides populations obtained from MSJ and Citrus paradise Macf (PTY), and also revealed weak genetic differentiation between the C. gloeosporioides populations obtained from Citrus sinensis Osbeck (QC), WG, and BDZ. The AMOVA test showed that the levels of genetic differentiation for C. gloeosporioides were 19% and 81% among and within geographic populations, respectively. It also showed that C. gloeosporioides had levels of genetic differentiation among and within host populations of 12% and 88%, respectively. The Mantel test showed that the genetic distance was not linearly correlated with geographical distance and the haplotype phylogenetic analysis showed that C. gloeosporioides from different regions and hosts were scattered in the phylogenetic tree, implying that the genetic differentiation was independent of host variety and geographical origin. We speculated that genetic differentiation may be mainly due to gene mutation, gene recombination, or gene migration within native populations and has nothing to do with natural selection triggered by geography or host variety.

Genomic Analyses Implicate the Amazon-Orinoco Plume as the Driver of Cryptic Speciation in a Swimming Crab.

The Amazon-Orinoco plume (AOP) is the world's largest freshwater and sediment discharge into the ocean. Previous studies limited to mtDNA suggest that the swimming crab Callinectes ornatus Ordway, 1863 exists as two distinct genetic clusters separated by the AOP. However, questions concerning migration, diversification time, and species delimitation are unresolved. Densely sampling markers across the genome (SNPs) could elucidate the evolutionary processes within this species. Here, we combined mtDNA data and ddRAD-seq to explore the diversification patterns and processes within the swimming crab C. ornatus. We show great genetic differentiation between groups on the north and south sides of the plume but also signs of hybridization. Demographic modeling indicates the divergence between groups starting around 8 Mya following the AOP's formation. After a period of isolation, we detect two incidences of secondary contact with stronger migration in concordance with the North Brazil Current flow. Our results suggest speciation with gene flow explained by the interplay among the AOP, oceanographic currents, and long larval dispersal. This work represents the first investigation employing ddRAD-seq in a marine invertebrate species with distribution encompassing the north and south Atlantic and sheds light on the role of the AOP in the diversification of a marine species.

Genetic Relationships of Puccinia striiformis f. sp. tritici in Southwestern and Northwestern China.

ABSTRACTWheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a crucial disease for wheat worldwide and constantly threatens wheat production in southwestern and northwestern China, where the environment is a good fit for Pst oversummering and overwintering. However, the underlying genetic dynamics of spring epidemic Pst populations across large areas of continuous planting in the southwestern and northwestern regions are poorly understood. A total of 2,103 Pst isolates were sampled in the spring of 2019 from the two agroecosystems and grouped into three horizontal spatial scales (countywide, provincial, and regional subpopulations) and two vertical spatial scales that consisted of elevational and geomorphic subpopulations. A total of 776 multilocus genotypes were identified, with the highest genetic diversity found in the northern and Sichuan populations, particularly in the Ningxia and Sichuan Basins, while the lowest genetic diversity was found in the Yunnan and Guizhou populations. Multivariate discriminant analysis of principal components (DAPC) and STRUCTURE (STRUCTURE 2.3.4) analyses revealed variation in the genotypic compositions of the molecular groups on horizontal and vertical dimensions from north to south or vice versa and from low to high or vice versa, respectively. The regional neighbor-joining tree revealed three large spatial structures consisting of the southwestern, the northwestern, and the Xinjiang regions, while the Tibetan population connected the southwestern and northwestern regions. The isolates of the Sichuan Basin were scattered over the four quartiles by principal coordinate analysis, which indicated frequent genotype interchange with others. Greater genetic differentiation was observed between the southwestern and northwestern regions. Linkage equilibrium (P ≥ 0.05) was detected on different spatial scales, suggesting that Pst populations are using sexual reproduction or mixed reproduction (sexual and clonal reproduction) in southwestern and northwestern China.IMPORTANCE Understanding the epidemiology and population genetics of plant pathogens is crucial to formulate efficient predictions of disease outbreaks and achieve sustainable integrated disease management, especially for pathogens with migratory capability. Here, this study covers the genetic homogeneity and heterogeneity of different geographical Pst populations on broad to fine spatial scales from the key epidemic regions of the two agroecosystems in China, where wheat stripe rust occurs annually. We provide knowledge of the population genetics of Pst and reveal that, for instance, there is greater genetic diversity in northwestern China, there are close genetic relationships between Yunnan and Guizhou and between Gansu-Ningxia and Qinghai, and there are effects of altitude on genetic compositions, etc. All of these findings clarify the genetic relationships and expand the insights into the population dynamics and evolutionary mechanisms of Pst in southwestern and northwestern China, providing a theoretical basis for achieving sustainable control of wheat stripe rust in key epidemic regions.

Limited phylogeographic and genetic connectivity in Acacia species of low stature in an arid landscape.

Widespread plant species are expected to maintain genetic diversity and gene flow via pollen and seed dispersal. Stature is a key life history trait that affects seed and potentially pollen dispersal, with limited stature associated with limited dispersal and greater genetic differentiation. We sampled Hill’s tabletop wattle (Acacia hilliana) and curry wattle (Acacia spondylophylla), two co‐distributed, widespread, Acacia shrubs of low stature, across the arid Pilbara region of north‐western Australia. Using chloroplast sequence and nuclear microsatellite data we evaluated patterns of population genetic and phylogeographic diversity and structure, demographic signals, ratios of pollen to seed dispersal, evidence for historical refugia, and association between elevation and diversity. Results showed strong phylogeographic (chloroplast, G ST = 0.831 and 0.898 for A. hilliana and A. spondylophylla, respectively) and contemporary (nuclear, F ST = 0.260 and 0.349 for A. hilliana and A. spondylophylla, respectively) genetic structure in both species. This indicates limited genetic connectivity via seed and pollen dispersal associated with Acacia species of small stature compared to taller tree and shrub acacias across the Pilbara bioregion. This effect of stature on genetic structure is superimposed on moderate levels of genetic diversity that were expected based on widespread ranges (haplotype diversity h = 25 and 12; nuclear diversity He = 0.60 and 0.47 for A. hilliana and A. spondylophylla, respectively). Contemporary genetic structure was congruent at the greater landscape scale, especially in terms of strong genetic differentiation among geographically disjunct populations in less elevated areas. Measures of diversity and connectivity were associated with traits of greater geographic population proximity, population density, population size, and greater individual longevity, and some evidence for range expansion in A. hilliana. Results illustrate that low stature is associated with limited dispersal and greater patterns of genetic differentiation for congenerics in a common landscape and highlight the complex influence of taxon‐specific life history and ecological traits to seed and pollen dispersal.

A chromosome-level genome of the human blood fluke Schistosoma japonicum identifies the genomic basis of host-switching.

The evolution and adaptation of S.japonicum, a zoonotic parasite that causes human schistosomiasis, remain unclear because of the lack of whole-genome data. We construct a chromosome-level S.japonicum genome and analyze it together with 72 samples representing six populations of the entire endemic region. We observe a Taiwan zoophilic lineage splitting from zoonotic populations ∼45,000 years ago, consistent with the divergent history of their intermediate hosts. Interestingly, we detect a severe population bottleneck in S.japonicum, largely coinciding with human history in Asia during the last glacial maximum. We identify several genomic regions underlying natural selection, including GATAD2A and Lmln, both showing remarkable differentiation among different areas. RNAi knockdown suggests association of GATAD2A with parasite development and infection in definitive hosts, while Lmln relates to the specificity of the intermediate hosts. Our study provides insights into the evolution of S.japonicum and serves as a resource for further studies.

Assessment of variability among morphological and molecular characters in wild populations of mint [Mentha longifolia (L.) L.] germplasm

Mentha longifolia is an important medicinal and aromatic perennial herb that exhibits wide distribution range from sub-tropical to temperate regions. In the present study, agro-morphological traits and genetic differences in 19 different populations of M. longifolia were studied to evaluate the level and extent of its diversity. Analysis of variance (ANOVA) showed that the different phenotypic characters show considerable differences among various populations and was significant at p < 0.05. Molecular diversity analysis performed by using arbitrary amplified eleven ISSR primers generated a total of 121 amplicons that range within the size of 200–2500 base pairs (bp). Each primer on average generated 11 amplicons with percentage polymorphism being 100. The analysis of molecular variance (AMOVA) showed more (64%) among population genetic diversity and less (36%) within the populations. Greater genetic differentiation (Gst = 0.6852) among these populations occurs due to low gene flow (Nm = 0.2297) and greater habitat variability. Geographic and genetic distances were positively correlated according to Mantel’s test. In order to remove any kind of biases, we used R software to perform cluster and redundancy analysis to analyse the extent of relatedness among studied populations. In terms of morphological and molecular aspects, the populations were grouped into four and five clusters respectively based on hierarchical clustering method. The results demonstrated that M. longifolia displays a great degree of morphological and genetic variation and can be utilized in breeding, genetic improvement, and gene bank conservation programmes in future.

The Centre–Periphery Model, a Possible Explanation for the Distribution of Some Pinus spp. in the Sierra Madre Occidental, Mexico

Genetic diversity is key to survival of species. In evolutionary ecology, the general centre–periphery theory suggests that populations of species located at the margins of their distribution areas display less genetic diversity and greater genetic differentiation than populations from central areas. The aim of this study was to evaluate the genetic diversity and differentiation in six of the main pine species of the Sierra Madre Occidental (northern Mexico). The species considered were Pinus arizonica, P. cembroides, P. durangensis, Pinus engelmannii, P. herrerae and P. leiophylla, which occur at the margins and centre of the geographic distribution. We sampled needles from 2799 individuals belonging to 80 populations of the six species. We analysed amplified fragment length polymorphisms (AFLPs) to estimate diversity and rarity indexes, applied Principal Coordinate Analysis (PCoA), and used the Kruskal–Wallis test to detect genetic differences. Finally, we calculated Spearman’s correlation for association between variables. The general centre–periphery model only explained the traits in P. herrerae. The elevation gradient was an important factor that influenced genetic diversity. However, for elevation as partitioning criterion, most populations showed a central distribution. This information may be useful for establishing seed collections of priority individuals for maintenance in germplasm banks and their subsequent sustainable use.

Tracking the desert's edge with a Pleistocene relict

In addition to the Sky Islands of the southwestern U.S. and northwestern Mexico, a series of 900–1200 m desert peaks surrounded by arid lowlands support temperate affiliated species at their summits. The presence of disjunct long-lived plant taxa on under-explored desert mountains, especially Isla Tiburón at 29° latitude in the Gulf of California, suggests a more southerly extent of Ice Age woodlands than previously understood. The phylogeography of the desert edge species Canotia holacantha (Celastraceae) was investigated to test the hypothesis that insular desert peak populations represent remnants of Pleistocene woodlands rather than recent dispersal events. Sequences of four chloroplast DNA regions totaling 2032 bp were amplified from 74 individuals of 14 populations across the entire range of C. holacantha as well as nine individuals that represented the other two species in its clade (C. wendtii and Acanthothamnus aphyllus) and two outgroups. Results suggest that a Canotia common ancestor occurred on the landscape, which underwent a population contraction ca. 15 kya. The Isla Tiburón C. holacantha population and the Chihuahuan Desert microendemic C. wendtii have the greatest genetic differentiation, are sister to one another, and basal to all other Canotia populations. Three haplotypes within C. holacantha were recovered, which correspond to regional geography and thus identified as the Arizona, Sonora, and Tiburón haplotypes, within which Acanthothamnus aphyllus is nested rather than as a sister genus. These results indicate a once broad distribution of Canotia/Acanthothamnus when the current peripheral desert ecotone habitat was more widespread during the Pleistocene, now present in relict populations on the fringes of the southern desert, in the Chihuahuan Desert, with scattered populations on desert peaks, and a common or abundant distribution at the northern boundary of the Sonoran Desert. These results suggest Canotia has tracked the shift of the desert's edge both in latitude and elevation since the end of the last Ice Age.

Maine's Bumble Bees (Hymenoptera: Apidae)-Part 2: Comparisons of a Common (Bombus ternarius) and a Rare (Bombus terricola) Species.

As part of a quantitative survey of Maine's bumble bee fauna (Butler et al. 2021), we compared and contrasted genetic diversity, parasite and pathogen burdens, and pesticide exposure of the relatively common Bombus ternarius Say, 1937 and the spatially rare Bombus terricola Kirby, 1837. We recorded 11 Bombus species at 40 survey sites across three Maine ecoregions, and B. ternarius was the most common species, while B. terricola was spatially rare. Nonmetric multidimensional scaling indicated that B. terricola was associated with higher elevation sites in Maine, while B. ternarius was more broadly distributed in the state. Pollinator networks constructed for each bee indicated B. ternarius foraged on more plant species than B. terricola, but that there was considerable overlap (73%) in plant species visited. Genetic diversity was greater in the spatially restricted B. terricola, whereas the widely distributed B. ternarius was characterized by greater genetic differentiation among regions. Bombus terricola had higher molecular marker levels of the microsporidian fungi Nosema spp. and the trypanosome Crithidia spp., and both species had high levels of Trypanosoma spp. exposure. No Western Honey Bee (Apis mellifera, Linnaeus, 1758) viruses were detected in either species. Pesticides were not detected in pollen samples collected from workers of either species, and B. ternarius worker tissue samples exhibited only trace levels of diflubenzuron.

Population structure and phylogenetic relationships in Brassica rapa L. subspecies by using isozyme markers.

The present study aimed to assess population structure and phylogenetic relationships of nine subspecies of Brassica rapa L. represented with thirty-five accessions cover a wide range of species distribution area using isozyme analysis in order to select more diverse accessions as supplementary resources that can be utilized for improvement of B. napus. Enzyme analysis resulted in detecting 14 putative polymorphic loci with 27 alleles. Mean allele frequency 0.04 (rare alleles) was observed in Cat4A and Cat4B in sub species Oleifera accession CR 2204/79 and in subspecies trilocularis accessions CR 2215/88 and CR 2244/88. The highest genetic diversity measures were observed in subspecies dichotoma, accession CR 1585/96 (the highest average of observed (H0) and expected heterozygosity (He), and number of alleles per locus (Ae)). These observations make this accession valuable genetic resource to be included in breeding programs for the improvement of oilseed B. napus. The average fixation index (F) is significantly higher than zero for the analysis accessions indicating a significant deficiency of heteozygosity. The divergence among subspecies indicated very great genetic differentiation (FST = 0.8972) which means that about 90% of genetic diversity is distributed among subspecies, while 10% of the diversity is distributed within subspecies. This coincides with low value of gene flow (Nm = 0.0287). B. rapa ssp. oleifera (turnip rape) and B. rapa ssp. trilocularis (sarson) were grouped under one cluster which coincides with the morphological classification.

Genetic and ecological evidence of long‐term translocation success of the federally endangered Stephens' kangaroo rat

AbstractThe efficacy of translocation as a method for conserving species in peril has not been fully evaluated. Post‐release monitoring rarely involves long‐term assessments and initial success metrics may not translate to population viability. In particular, genetic factors may play a critical role in fitness following release as founder effect, genetic drift, inbreeding depression and outbreeding depression can influence extinction risk. As part of a multi‐year recovery effort, we translocated populations of the endangered Stephens' kangaroo rat (Dipodomys stephensi; SKR), in order to restore population connectivity. Here we evaluate the success of the translocation efforts through long‐term population estimation and genetic analyses. We conducted post‐release assessments for 9 years, and used Bayesian clustering analysis and principal components analysis (PCA) of 24 microsatellite markers developed for this species to assess genetic admixture between source and translocated populations. Demographic results indicate long‐term translocation success, as evidenced by founder survival and establishment, and population growth and regulation. Genetic results show admixture at the release site between genetically discrete source populations, provide definitive evidence that translocated individuals, not immigrants, produced offspring at the release site, that these offspring successfully reproduced and that even with moderate to great genetic differentiation of source populations, outbreeding depression was not detected. Despite the historical failure of heteromyid translocation efforts, our long‐term study illustrates how the development of species‐specific best practices led to an effective strategy for SKR recovery. More broadly, our results suggest efforts that use a systematic hypothesis‐testing framework alongside long‐term monitoring offer great promise in improving translocation outcomes.

Genetic diversity and genetic structure of &amp;lt;italic&amp;gt;Coilia nasus taihuensis&amp;lt;/italic&amp;gt; populations in Jiangsu Province based on mtDNA control region sequences

<italic>Coilia nasus taihuensis</italic> is the dominant species in freshwater lake fish community of the lower reaches of the Yangtze River and Huaihe River, and it is also an important fishing target. In order to better understand the genetic diversity and genetic structure of <italic>C</italic>. <italic>nasus taihuensis</italic> populations in freshwater lakes, we analyzed the genetic variation of mitochondrial DNA loop region among six wild lake populations (Ge Lake, Tai Lake, Gaoyou Lake, Baima Lake, Hongze Lake and Luoma Lake) of <italic>C</italic>. <italic>nasus taihuensis</italic> in Jiangsu Province. By means of PCR amplification and sequencing, the full length of D-loop sequences were obtained and then used for genetic diversity and genetic structure analysis. A total of 103 variable sites and 92 haplotypes were detected in 214 individuals. The haplotype diversity and nucleotide diversity of six populations varied from 0.726 to 0.951, from 0.005 52 to 0.005 52, respectively. Meanwhile, the haplotype diversity and nucleotide diversity of total populations were 0.857 and 0.007 29, respectively. Results suggested that the haplotype diversity of <italic>C</italic>. <italic>nasus taihuensis</italic> was high, while the nucleotide diversity was low. AMOVA analysis indicated that 6.20% of the molecular variation occurred between populations, and 93.80% occurred within populations, suggesting that great genetic differentiation existed among certain populations. The genetic differentiation index (<italic>F</italic>_st) value of total populations was 0.061 99 (<italic>P</italic><0.01), and the pairwise <italic>F</italic>_st values among populations indicated that there was significant genetic differentiation between Ge Lake population and the other five populations, and there was no significant genetic differentiation among the five populations. The neighbor-joining phylogenetic tree and parsimony network of haplotypes indicated that individuls of <italic>C</italic>. <italic>nasus taihuensis</italic> were divided into two lineages without correlation with geographical populations. The neutrality tests suggested <italic>C</italic>. <italic>nasus taihuensis</italic> population had undergone population expansion in evolutionary history, and the population expansion appeared in 0.089-0.16 million years ago. The research results showed that the genetic diversity of <italic>C</italic>. <italic>nasus taihuensis</italic> was abundant in Jiangsu Province. The Ge Lake population owned multiple peculiar haplotypes, and there were significant genetic differences between Ge Lake population and the other five lake populations. So, the Ge Lake population should be managed as an independent unit, and the other five populations should be managed and utilized as a whole unit.