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1.
Am J Bot ; 110(7): e16201, 2023 07.
Article in English | MEDLINE | ID: mdl-37306119

ABSTRACT

PREMISE: Pollen movement is a crucial component of dispersal in seed plants. Although pollen dispersal is well studied, methodological constraints have made it challenging to directly track pollen flow within multiple populations across landscapes. We labeled pollen with quantum dots, a new technique that overcomes past limitations, to evaluate the spatial scale of pollen dispersal and its relationship with conspecific density within 11 populations of Clarkia xantiana subsp. xantiana, a bee-pollinated annual plant. METHODS: We used experimental arrays in two years to track pollen movement across distances of 5-35 m within nine populations and across distances of 10-70 m within two additional populations. We tested for distance decay of pollen dispersal, whether conspecific density modulated dispersal distance, and whether dispersal kernels varied among populations across an environmentally complex landscape. RESULTS: Labeled pollen receipt did not decline with distance over 35 m within eight of nine populations or over 70 m within either of two populations. Pollen receipt increased with conspecific density. Overall, dispersal kernels were consistent across populations. CONCLUSIONS: The surprising uniformity in dispersal distance within different populations was likely influenced by low precipitation and plant density in our study years. This suggests that spatiotemporal variation in the abiotic environment substantially influences the extent of gene flow within and among populations.


Subject(s)
Pollination , Quantum Dots , Bees , Animals , Pollen/genetics , Seeds/genetics , Gene Flow , Microsatellite Repeats , Genetic Variation
2.
Am Nat ; 201(1): 52-64, 2023 01.
Article in English | MEDLINE | ID: mdl-36524929

ABSTRACT

AbstractPollen dispersal is a key evolutionary and ecological process, but the degree to which variation in the density of concurrently flowering conspecific plants (i.e., coflowering density) shapes pollination patterns remains understudied. We monitored coflowering density and corresponding pollination patterns of the insect-pollinated palm Oenocarpus bataua in northwestern Ecuador and found that the influence of coflowering density on these patterns was scale dependent: high neighborhood densities were associated with reductions in pollen dispersal distance and gametic diversity of progeny arrays, whereas we observed the opposite pattern at the landscape scale. In addition, neighborhood coflowering density also impacted forward pollen dispersal kernel parameters, suggesting that low neighborhood densities encourage pollen movement and may promote gene flow and genetic diversity. Our work reveals how coflowering density at different spatial scales influences pollen movement, which in turn informs our broader understanding of the mechanisms underlying patterns of genetic diversity and gene flow within populations of plants.


Subject(s)
Arecaceae , Pollination , Pollen/genetics , Gene Flow , Reproduction/genetics , Arecaceae/genetics , Genetic Variation , Microsatellite Repeats
3.
BMC Genomics ; 23(1): 750, 2022 Nov 12.
Article in English | MEDLINE | ID: mdl-36368918

ABSTRACT

BACKGROUND: Evolutionary divergence and speciation often occur at a slower rate in the marine realm due to the higher potential for long-distance reproductive interaction through larval dispersal. One common evolutionary pattern in the Indo-Pacific, is divergence of populations and species at the peripheries of widely-distributed organisms. However, the evolutionary and demographic histories of such divergence are yet to be well understood. Here we address these issues by coupling genome-wide SNP data with mitochondrial DNA sequences to test the patterns of genetic divergence and possible secondary contact among geographically distant populations of the highly valuable spiny lobster Panulirus homarus species complex, distributed widely through the Indo-Pacific, from South Africa to the Marquesas Islands. RESULT: After stringent filtering, 2020 SNPs were used for population genetic and demographic analyses, revealing strong regional structure (FST = 0.148, P < 0001), superficially in accordance with previous analyses. However, detailed demographic analyses supported a much more complex evolutionary history of these populations, including a hybrid origin of a North-West Indian Ocean (NWIO) population, which has previously been discriminated morphologically, but not genetically. The best-supported demographic models suggested that the current genetic relationships among populations were due to a complex series of past divergences followed by asymmetric migration in more recent times. CONCLUSION: Overall, this study suggests that alternating periods of marine divergence and gene flow have driven the current genetic patterns observed in this lobster and may help explain the observed wider patterns of marine species diversity in the Indo-Pacific.


Subject(s)
Palinuridae , Animals , Palinuridae/genetics , Nephropidae/genetics , Polymorphism, Single Nucleotide , Genome , Gene Flow , DNA, Mitochondrial/genetics , Phylogeny , Genetic Variation
4.
Sci Rep ; 12(1): 16783, 2022 10 06.
Article in English | MEDLINE | ID: mdl-36202873

ABSTRACT

The emergence of high resolution population genetic techniques, such as genotyping-by-sequencing (GBS), in combination with recent advances in particle modelling of larval dispersal in marine organisms, can deliver powerful new insights to support fisheries conservation and management. In this study, we used this combination to investigate the population connectivity of a commercial deep sea lobster species, the New Zealand scampi, Metanephrops challengeri, which ranges across a vast area of seafloor around New Zealand. This species has limited dispersal capabilities, including larvae with weak swimming abilities and short pelagic duration, while the reptant juvenile/adult stages of the lifecycle are obligate burrow dwellers with limited home ranges. Ninety-one individuals, collected from five scampi fishery management areas around New Zealand, were genotyped using GBS. Using 983 haplotypic genomic loci, three genetically distinct groups were identified: eastern, southern and western. These groups showed significant genetic differentiation with clear source-sink dynamics. The direction of gene flow inferred from the genomic data largely reflected the hydrodynamic particle modelling of ocean current flow around New Zealand. The modelled dispersal during pelagic larval phase highlights the strong connectivity among eastern sampling locations and explains the low genetic differentiation detected among these sampled areas. Our results highlight the value of using a transdisciplinary approach in the inference of connectivity among populations for informing conservation and fishery management.


Subject(s)
Gene Flow , Nephropidae , Animals , Fisheries , Genetics, Population , Haplotypes , Humans , Larva/genetics
5.
Mol Biol Rep ; 49(11): 11209-11214, 2022 Nov.
Article in English | MEDLINE | ID: mdl-36136213

ABSTRACT

BACKGROUND: Cylicodiscus gabunensis (Fabaceae) or 'Okan' is a Central African multipurpose timber species that is used for heavy construction and traditional medicine. Despite being currently heavily exploited, the species shows a low population density and a natural regeneration deficit in dense forest. METHODS AND RESULTS: We aimed to characterize polymorphic microsatellite markers that can be used to study patterns of genetic structure and gene flow (mating system, pollen and seed dispersal and inbreeding depression) and ultimately, help to develop sustainable forest management practices. We developed 24 polymorphic markers that can be amplified in three PCR multiplexes that were tested in 647 individuals of C. gabunensis from three populations. The number of alleles ranged from 4 to 27 and the average observed and expected heterozygosity across loci and populations were Ho = 0.585 (0.081-0.936) and He = 0.510 (0.076-0.914), respectively. CONCLUSIONS: This set of markers is a useful tool for exploring intra-specific diversity, genetic structure and gene flow of C. gabunensis.


Subject(s)
Fabaceae , Trees , Humans , Male , Trees/genetics , Fabaceae/genetics , Genetics, Population , Microsatellite Repeats/genetics , Gene Flow
6.
Science ; 377(6609): 982-987, 2022 08 26.
Article in English | MEDLINE | ID: mdl-36007054

ABSTRACT

We present the first ancient DNA data from the Pre-Pottery Neolithic of Mesopotamia (Southeastern Turkey and Northern Iraq), Cyprus, and the Northwestern Zagros, along with the first data from Neolithic Armenia. We show that these and neighboring populations were formed through admixture of pre-Neolithic sources related to Anatolian, Caucasus, and Levantine hunter-gatherers, forming a Neolithic continuum of ancestry mirroring the geography of West Asia. By analyzing Pre-Pottery and Pottery Neolithic populations of Anatolia, we show that the former were derived from admixture between Mesopotamian-related and local Epipaleolithic-related sources, but the latter experienced additional Levantine-related gene flow, thus documenting at least two pulses of migration from the Fertile Crescent heartland to the early farmers of Anatolia.


Subject(s)
Farmers , Gene Flow , Human Migration , Archaeology , Armenia , Cyprus , DNA, Ancient , Farmers/history , History, Ancient , Human Migration/history , Mesopotamia
7.
Science ; 377(6609): eabm4247, 2022 08 26.
Article in English | MEDLINE | ID: mdl-36007055

ABSTRACT

By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra-West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe.


Subject(s)
Gene Flow , Genome, Human , Human Migration , Asia , Balkan Peninsula , Europe , History, Ancient , Human Migration/history , Humans , White People/genetics
8.
Mol Ecol ; 31(20): 5182-5200, 2022 10.
Article in English | MEDLINE | ID: mdl-35960266

ABSTRACT

In marine species experiencing intense fishing pressures, knowledge of genetic structure and local adaptation represent a critical information to assist sustainable management. In this study, we performed a landscape genomics analysis in the American lobster to investigate the issues pertaining to the consequences of making use of putative adaptive loci to reliably infer population structure and thus more rigorously delineating biological management units in marine exploited species. Toward this end, we genotyped 14,893 single nucleotide polymorphism (SNPs) in 4190 lobsters sampled across 96 sampling sites distributed along 1000 km in the northwest Atlantic in both Canada and the USA. As typical for most marine species, we observed a weak, albeit highly significant genetic structure. We also found that adaptive genetic variation allows detecting fine-scale population structure not resolved by neutral genetic variation alone. Using the recent genome assembly of the American lobster, we were able to map and annotate several SNPs located in functional genes potentially implicated in adaptive processes such as thermal stress response, salinity tolerance and growth metabolism pathways. Taken together, our study indicates that weak population structure in high gene flow systems can be resolved at various spatial scales, and that putatively adaptive genetic variation can substantially enhance the delineation of biological management units of marine exploited species.


Subject(s)
Genomics , Nephropidae , Animals , Gene Flow , Genotype , Nephropidae/genetics , Polymorphism, Single Nucleotide/genetics
9.
Sci Rep ; 12(1): 11699, 2022 07 09.
Article in English | MEDLINE | ID: mdl-35810208

ABSTRACT

Dactylorhiza hatagirea (D. Don) Soo is medicinally important herb, which is widely used in ayurveda, unani, and folk/traditional medicine system to cure diseases. Due to its immense ethno-botanical properties, the trade of D. hatagirea is estimated to be USD 1 billion/year in India. Unfortunately, due to overexploitation of the herb from the wild, has resulted in dwindling of its populations in their natural habitats, which has led to its critically endangered status. Molecular genetic studies are still scarce in D. hatagirea, therefore, in current study, genetic diversity and population structure analysis was carried out of 10 populations (48 individuals) collected from three cold desert regions (2527 m-3533 m amsl) of Himachal Pradesh. Mean observed heterozygosity (Ho) and expected heterozygosity (He) was recorded 0.185 and 0.158. The maximum values for Fst (fixation index) and Nm (gene flow) were recorded 0.945 at locus KSSR14 and 1.547 at locus KSSR 4 respectively. Mean genetic differentiation (Fst) coefficient was estimated to 0.542. Overall, low levels of genetic diversity was recorded in the populations of D. hatagirea, might be due to habitat specificity (alpine meadows ecosystem; humid laden undulating habitat), restricted distribution and high anthropogenic activities. However, two populations viz., Bathad and Rangrik were recorded with high diversity and largest number of private alleles, stipulates that these populations might have high evolutionary significance and response to selection. Dendrogram analysis revealed that the populations of D. hatagirea were clustered into four major clusters, which was supported by Bayesian based STRUCTURE predictions. Clustering pattern of majority individuals of different populations revealed consistency with their geographic origin. Outcomes of current study reveals the status of genetic diversity and population structure of endangered D. hatagirea, which can be futuristically utilised for appropriate planning of conservation strategies.


Subject(s)
Ecosystem , Orchidaceae , Bayes Theorem , Gene Flow , Genetic Variation , Genetics, Population , Humans , Microsatellite Repeats/genetics , Orchidaceae/genetics
10.
Mol Biol Rep ; 49(2): 1181-1189, 2022 Feb.
Article in English | MEDLINE | ID: mdl-34981338

ABSTRACT

BACKGROUND: Salvia macrosiphon is an aromatic perennial species of Lamiaceae family that grows naturally in different parts of Iran. This herb is widely used in folk and modern medicine. Although in Flora Iranica and Flora of Iran, no infraspecific taxonomic rank has been detected for S. macrosiphon, some infraspecific taxonomic ranks have been reported. In the current study, we evaluated the genetic diversity and structure of 11 populations of this species to detect inter and intrapopulation genetic diversity and to survey the possibility of infraspecific taxonomic ranks in this species. METHODS AND RESULTS: We utilized the modified C-TAB protocol for DNA extraction and amplified the genomes using several SCoT molecular markers. We calculated of genetic diversity and polymorphism parameters using GenAlex 6.4, Geno-Dive ver.2, PopGene, PopART and Structure 2.3.4. The parameters of genetic polymorphism differed between the populations. Moreover, a low rate of gene flow supported a moderate level of population's genetic diversity and differentiation. According to haplotypes network (TCS) analysis, a high level of genetic mutation has occurred among the individuals of some populations leading to high intrapopulation diversity. On the basis of structure analysis and Nei's genetic distance, the examined populations were classified into four genotypes. CONCLUSIONS: The clustering pattern of the populations in each group was not related to geographical distance or phytogeography. It seems that the wide geographic distribution, a small gene flow rate and the occurrence of a high level of genetic mutation lead to infraspecific genetic differentiation in the species and we suppose some infraspecific ranks exist for it.


Subject(s)
Genetic Markers/genetics , Salvia/genetics , Classification/methods , Cluster Analysis , Gene Flow/genetics , Genetic Variation/genetics , Genotype , Geography , Iran , Lamiaceae/genetics , Microsatellite Repeats/genetics , Phylogeny , Polymorphism, Genetic/genetics , Salvia/metabolism
11.
Plant Biol (Stuttg) ; 24(1): 185-191, 2022 Jan.
Article in English | MEDLINE | ID: mdl-34634170

ABSTRACT

Endemic species distributed in fragmented habitats are highly vulnerable to extinction because they may have low genetic diversity. However, some life-history traits can mitigate the effect of genetic drift on populations. We analysed the level and distribution of genetic variation and ancestral population size of Yucca capensis, a long-lived endemic plant of the Baja California Peninsula, Mexico. Its populations are scattered across a habitat that is suffering accelerated transformation. We used six nuclear microsatellites to genotype 224 individuals from 17 locations across the entire species' geographic range. We estimated polymorphisms, heterozygosity and genetic structure. We also evaluated the ancestral and recent effective size and time since the population started to change. We found high heterozygosity, high polymorphism and low differentiation among locations, suggesting a panmictic population across the range. We also detected a large ancestral effective population size, which suffered a strong reduction in the Mid-Holocene. Despite changes in environmental conditions caused by habitat modification, the high diversity and low differentiation in Y. capensis may result from its large ancestral effective size and life-history traits, such as plant longevity, clonal growth and mating system, which reduce the rate of loss of genetic variation. However, the dependence on a specialist pollinator that displays short flight range can reduce gene flow among the plant populations and could, shortly, lead them into an extinction vortex.


Subject(s)
Asparagaceae , Yucca , Ecosystem , Gene Flow , Genetic Variation , Genetics, Population , Mexico , Microsatellite Repeats/genetics , Trees/genetics
12.
Mol Biol Rep ; 49(1): 805-810, 2022 Jan.
Article in English | MEDLINE | ID: mdl-34689293

ABSTRACT

BACKGROUND: Campanula glomerata L. (Campanulaceae) is a self-incompatible, insect-pollinated herb occurring in calcareous grasslands, and is declining and (critically) endangered in many parts of its European distribution range. It often exists as small and isolated populations. A recovery plan of C. glomerata has been implemented in southern Belgium, involving plant translocations. METHODS AND RESULTS: We developed microsatellite markers using an enriched genomic library and characterized 16 loci in 111 individuals from eight populations. These 16 loci were highly polymorphic, with 11 to 31 alleles per locus for a total of 329 alleles, and expected heterozygosity (He) ranging from 0.470 to 0.938. CONCLUSIONS: These highly polymorphic loci constitute a promising tool for detailed genetic analyses: assigning individuals to distinct multilocus genotypes will allow quantifying pollen dispersal, clonal propagation and sexual recruitment and identifying admixed seed progeny and their pollen donors. Evaluating the genetic status of existing populations and a genetic monitoring of the translocated populations will contribute to optimize success in restoring viable and evolutionary resilient populations.


Subject(s)
Campanulaceae/genetics , Genes, Plant , Microsatellite Repeats/genetics , Polymorphism, Genetic , Seeds/genetics , Alleles , Endangered Species , Gene Flow , Genetic Loci , Genomic Library , Genotype , Grassland , Pollen/genetics
13.
Nat Commun ; 12(1): 5929, 2021 10 12.
Article in English | MEDLINE | ID: mdl-34642339

ABSTRACT

Arab populations are largely understudied, notably their genetic structure and history. Here we present an in-depth analysis of 6,218 whole genomes from Qatar, revealing extensive diversity as well as genetic ancestries representing the main founding Arab genealogical lineages of Qahtanite (Peninsular Arabs) and Adnanite (General Arabs and West Eurasian Arabs). We find that Peninsular Arabs are the closest relatives of ancient hunter-gatherers and Neolithic farmers from the Levant, and that founder Arab populations experienced multiple splitting events 12-20 kya, consistent with the aridification of Arabia and farming in the Levant, giving rise to settler and nomadic communities. In terms of recent genetic flow, we show that these ancestries contributed significantly to European, South Asian as well as South American populations, likely as a result of Islamic expansion over the past 1400 years. Notably, we characterize a large cohort of men with the ChrY J1a2b haplogroup (n = 1,491), identifying 29 unique sub-haplogroups. Finally, we leverage genotype novelty to build a reference panel of 12,432 haplotypes, demonstrating improved genotype imputation for both rare and common alleles in Arabs and the wider Middle East.


Subject(s)
Chromosomes, Human, Y , Genome, Human , Haplotypes , Human Migration/history , Phylogeny , Africa , Alleles , Arabs/genetics , Asia , DNA, Mitochondrial/genetics , Datasets as Topic , Europe , Female , Gene Flow , Gene Frequency , History, 21st Century , History, Ancient , History, Medieval , Humans , Male , Phylogeography , Qatar , Sequence Analysis, DNA , Whole Genome Sequencing
14.
Nat Commun ; 12(1): 5317, 2021 09 07.
Article in English | MEDLINE | ID: mdl-34493715

ABSTRACT

After the main Out-of-Africa event, humans interbred with Neanderthals leaving 1-2% of Neanderthal DNA scattered in small fragments in all non-African genomes today. Here we investigate what can be learned about human demographic processes from the size distribution of these fragments. We observe differences in fragment length across Eurasia with 12% longer fragments in East Asians than West Eurasians. Comparisons between extant populations with ancient samples show that these differences are caused by different rates of decay in length by recombination since the Neanderthal admixture. In concordance, we observe a strong correlation between the average fragment length and the mutation accumulation, similar to what is expected by changing the ages at reproduction as estimated from trio studies. Altogether, our results suggest differences in the generation interval across Eurasia, by up 10-20%, over the past 40,000 years. We use sex-specific mutation signatures to infer whether these changes were driven by shifts in either male or female age at reproduction, or both. We also find that previously reported variation in the mutational spectrum may be largely explained by changes to the generation interval. We conclude that Neanderthal fragment lengths provide unique insight into differences among human populations over recent history.


Subject(s)
DNA, Ancient/analysis , Gene Flow , Genome, Human , Mutation , Neanderthals/genetics , Animals , Asia , Crosses, Genetic , Europe , Female , History, 21st Century , History, Ancient , Humans , Male , Polymorphism, Restriction Fragment Length
15.
Nature ; 598(7882): 629-633, 2021 10.
Article in English | MEDLINE | ID: mdl-34526723

ABSTRACT

During the Early Bronze Age, populations of the western Eurasian steppe expanded across an immense area of northern Eurasia. Combined archaeological and genetic evidence supports widespread Early Bronze Age population movements out of the Pontic-Caspian steppe that resulted in gene flow across vast distances, linking populations of Yamnaya pastoralists in Scandinavia with pastoral populations (known as the Afanasievo) far to the east in the Altai Mountains1,2 and Mongolia3. Although some models hold that this expansion was the outcome of a newly mobile pastoral economy characterized by horse traction, bulk wagon transport4-6 and regular dietary dependence on meat and milk5, hard evidence for these economic features has not been found. Here we draw on proteomic analysis of dental calculus from individuals from the western Eurasian steppe to demonstrate a major transition in dairying at the start of the Bronze Age. The rapid onset of ubiquitous dairying at a point in time when steppe populations are known to have begun dispersing offers critical insight into a key catalyst of steppe mobility. The identification of horse milk proteins also indicates horse domestication by the Early Bronze Age, which provides support for its role in steppe dispersals. Our results point to a potential epicentre for horse domestication in the Pontic-Caspian steppe by the third millennium BC, and offer strong support for the notion that the novel exploitation of secondary animal products was a key driver of the expansions of Eurasian steppe pastoralists by the Early Bronze Age.


Subject(s)
Dairying/history , Human Migration , Proteome , Animals , Archaeology , Asia , Dental Calculus/metabolism , Domestication , Europe , Gene Flow , Grassland , History, Ancient , Horses , Humans , Milk
16.
PLoS One ; 16(8): e0255776, 2021.
Article in English | MEDLINE | ID: mdl-34388195

ABSTRACT

The estimation of recent gene flow rates among vast and often weakly genetically differentiated tree populations remains a great challenge. Yet, empirical information would help understanding the interaction between gene flow and local adaptation in present-day non-equilibrium forests. We investigate here recent gene flow rates between two large native Scots pine (Pinus sylvestris L.) populations in central Iberian Peninsula (Spain), which grow on contrasting edaphic conditions six kilometers apart from each other and show substantial quantitative trait divergence in common garden experiments. Using a sample of 1,200 adult and offspring chloroplast-microsatellite haplotypes and a Bayesian inference model, we estimated substantial male gametic gene flow rates (8 and 21%) between the two natural populations, and even greater estimated immigration rates (42 and 64%) from nearby plantations into the two natural populations. Our results suggest that local pollen shedding within large tree populations does not preclude long-distance pollen immigration from large external sources, supporting the role of gene flow as a homogenizing evolutionary force contributing to low molecular genetic differentiation among populations of widely distributed wind-pollinated species. Our results also indicate the high potential for reproductive connectivity in large fragmented populations of wind-pollinated trees, and draw attention to a potential scenario of adaptive genetic divergence in quantitative traits under high gene flow.


Subject(s)
Gene Flow/genetics , Genetics, Population , Pinus sylvestris/genetics , Pollen/genetics , Forests , Genetic Variation/genetics , Haplotypes/genetics , Pollination/genetics , Spain
17.
Genes (Basel) ; 12(8)2021 08 20.
Article in English | MEDLINE | ID: mdl-34440453

ABSTRACT

A long-standing and unresolved issue in invasion biology concerns the rapid adaptation of invaders to nonindigenous environments. Mikania micrantha is a notorious invasive weed that causes substantial economic losses and negative ecological consequences in southern China. However, the contributions of gene flow, environmental variables, and functional genes, all generally recognized as important factors driving invasive success, to its successful invasion of southern China are not fully understood. Here, we utilized a genotyping-by-sequencing approach to sequence 306 M. micrantha individuals from 21 invasive populations. Based on the obtained genome-wide single nucleotide polymorphism (SNP) data, we observed that all the populations possessed similar high levels of genetic diversity that were not constrained by longitude and latitude. Mikania micrantha was introduced multiple times and subsequently experienced rapid-range expansion with recurrent high gene flow. Using FST outliers, a latent factor mixed model, and the Bayesian method, we identified 38 outlier SNPs associated with environmental variables. The analysis of these outlier SNPs revealed that soil composition, temperature, precipitation, and ecological variables were important determinants affecting the invasive adaptation of M. micrantha. Candidate genes with outlier signatures were related to abiotic stress response. Gene family clustering analysis revealed 683 gene families unique to M. micrantha which may have significant implications for the growth, metabolism, and defense responses of M. micrantha. Forty-one genes showing significant positive selection signatures were identified. These genes mainly function in binding, DNA replication and repair, signature transduction, transcription, and cellular components. Collectively, these findings highlight the contribution of gene flow to the invasion and spread of M. micrantha and indicate the roles of adaptive loci and functional genes in invasive adaptation.


Subject(s)
Adaptation, Physiological/genetics , Gene Flow/genetics , Mikania/genetics , Plant Weeds/genetics , China , Introduced Species , Metagenomics , Mikania/growth & development , Plant Weeds/growth & development
18.
New Phytol ; 232(1): 388-403, 2021 10.
Article in English | MEDLINE | ID: mdl-34143496

ABSTRACT

Topological cytonuclear discordance is commonly observed in plant phylogenetic and phylogeographic studies, yet few studies have attempted to detect two other forms of cytonuclear discordance (branch length and geographical) and to uncover the causes of the discordance. We used the whole nuclear and chloroplast genome data from 80 individual Asian butternuts to reveal the pattern and processes of cytonuclear discordance. Our findings indicate that the chloroplast genome had substantially deeper divergence (branch-length discordance) and a steeper cline in the contact zone (geographic discordance) compared with the nuclear genome. After various hypothesis have been tested, the results suggest that incomplete lineage sorting, positive selection and cytonuclear incompatibility are probably insufficient to explain this pattern. However, isolation-by-distance analysis and gene flow estimation point to a much higher level of gene flow by pollen compared with by seeds, which may have slowed down lineage divergence and mediated wider contact for nuclear genome compared with the chloroplast genome. Altogether, this study highlights a critical role of sex-biased dispersal in causing discordance between the nuclear and plastid genome of Asian butternuts. Given its ubiquity among plants, asymmetric gene flow should be given a high priority in future studies of cytonuclear discordance.


Subject(s)
Gene Flow , Genome, Chloroplast , Cell Nucleus/genetics , Phylogeny , Pollen/genetics , Seeds/genetics
19.
Am J Bot ; 108(6): 1016-1028, 2021 06.
Article in English | MEDLINE | ID: mdl-34114219

ABSTRACT

PREMISE: Pollinator foraging behavior can influence pollen dispersal and gene flow. In many plant species a pollinator trips a flower by applying pressure to release its sexual organs. We propose that differences in tripping rate among grooming pollinators could generate distinct pollen deposition curves, the pattern of pollen deposition over successive flowers visited. This study compares the pollen deposition curves of two grooming pollinators, a social bumble bee and a solitary leafcutting bee, with distinct tripping rates on Medicago sativa flowers. We predict a steeper deposition curve for pollen moved by leafcutting bees, the pollinator with the higher tripping rate. METHODS: Medicago sativa plants carrying a gene (GUS) whose product is easily detected by staining, were used as pollen donors. After visiting the GUS plants, a bee was released on a linear array of conventional M. sativa plants. The number of GUS pollen grains deposited over successive flowers visited or over cumulative distances was examined. Distinct mixed effect Poisson regression models, illustrating different rates of decay in pollen deposition, were fitted to the pollen data for each bee species. RESULTS: Pollen decay was steeper for leafcutting bees relative to bumble bees for both models of flowers visited and cumulative distance, as predicted by their higher tripping rate. CONCLUSIONS: This is the first report of a difference in pollen deposition curves between two bee species, both grooming pollinators. Such differences could lead to distinct impacts of bee species on gene flow, genetic differentiation, introgression, and ultimately speciation.


Subject(s)
Gene Flow , Pollination , Animals , Bees/genetics , Flowers , Medicago sativa/genetics , Pollen/genetics
20.
J Hum Evol ; 156: 103011, 2021 07.
Article in English | MEDLINE | ID: mdl-34102521

ABSTRACT

The period between 600 and 400 ka is a critical phase for human evolution in Europe. The south and northwest saw a dramatic increase in sites, the spread of handaxe technology alongside bone and wooden tool manufacture, efficient hunting techniques, and the use of fire. Lithic assemblages show considerable variation, including the presence/absence of handaxes and tool morphology. To explain this variation, we propose the Cultural Mosaic Model, which suggests that there is a range of expressions of the Acheulean, with local resources being instrumental in creating distinct material cultures with or without handaxes. We argue that if typologically and technologically distinct assemblage types are regionally distributed, chronologically separated, and persistent over time, then they are unlikely to be caused purely by raw material constraints or functional variation but rather reflect populations with different material cultures. We initially assess the model using British data. Britain was a northwestern peninsula of Europe, and oscillations in climate led to episodic occupation. The terraces of the pre-MIS 12 Bytham River provide a framework for dating occupation to MIS 13 and 15, while during MIS 11, archaeological sites with rich environmental records can be dated to substage level. We suggest there are six chronologically and typologically distinct assemblage types that reflect a series of population incursions into Britain. We review the broader European lithic record, which is consistent with the Cultural Mosaic Model. In developing the model, we suggest that during stable climate, localized cultures developed, while climatic change led to shifts in population, with increased knowledge exchange and gene flow. We suggest that group expression through material culture was an important stage in social development by promoting group cohesion, larger group size, better cooperation, improved knowledge transfer, and enabling populations to survive in larger foraging territories in northern Europe.


Subject(s)
Archaeology , Technology/history , Europe , Gene Flow , History, Ancient , Humans , Rivers
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