Sander vitreus) populations and a fourth reference population with low harvest levels over a 15‐year period in Mistassini Lake, Quebec. We also collected Indigenous knowledge (IK) surrounding concerns about these populations over time. Using ~9,000 SNPs, genomic metrics included changes in population structure, neutral genomic diversity, effective population size, and signatures of selection. Indigenous knowledge revealed overall reductions in body size and number of fish caught. Smaller body size, a small reduction in size‐at‐age, nascent changes to population structure (population differentiation within one river and homogenization between two others), and signatures of selection between historical and contemporary samples reflected coupled phenotypic and genomic change in the three harvested populations in both sexes, while no change occurred in the reference population. Sex‐specific analyses revealed differences in both body size and genomic metrics but were inconclusive about whether one sex was disproportionately affected. Although alternative explanations cannot be ruled out, our collective results are consistent with the hypothesis that genetic changes associated with harvesting may arise within 1–2.5 generations in long‐lived wild fishes. This study thus demonstrates the need to investigate concerns about harvest‐induced evolution quickly once they have been raised.The extent and rate of harvest‐induced genetic changes in natural populations may impact population productivity, recovery, and persistence. While there is substantial evidence for phenotypic changes in harvested fishes, knowledge of genetic change in the wild remains limited, as phenotypic and genetic data are seldom considered in tandem, and the number of generations needed for genetic changes to occur is not well understood. We quantified changes in size‐at‐age, sex‐specific changes in body size, and genomic metrics in three harvested walleye ( Catch p2.3We modeled both body size  and size‐at‐age in this study because we had a far greater sample size for body size estimates than aged samples, and mass estimates had not been correlated with historic aged samples. Thus, evaluating body size allowed us to investigate changes in length and mass on a per‐river, per‐sex, and per‐year basis.2.3.1iY) included the following.We used multiple regressions and ANOVA in R  method for 64 planned contrasts  was normally distributed such that:βcoefficients and modeled hyperpriors for age and sex by river. Location (southern rivers versus northern river) and history (contemporary versus historic samples) were coded as categorical variables.We used vague normal priors for allrjags and run.jags   to assess read‐quality before and after using cutadapt  and ‐p 4/6 (Icon–Perch merged); the numerator is the total number of populations required to have that locus, while the denominator is the total number of populations in the population map. All years and rivers were used initially to find the best‐supported population structure and to discover any changes that were occurring between rivers and years. Once the appropriate population structure was determined, Icon–Perch were merged (see Population structure section of Results below for a full explanation). No negative controls produced stacks, and all positive controls assigned to the correct populations using discriminant analysis of principal components (DAPC) in Adegenet  were determined from raw sequence reads using the  Martin,  to trim  Martin, , but we Jombart, . After q2.5FST) .To test our prediction that harvesting in the southern populations would change genetic population structure, potentially homogenizing structure between southern rivers over time, we assessed population structure using DAPC, ADMIXTURE  using plink v1.9  and reanalyzed population structure with DAPC. Since linked loci had no effect on structure, they were retained for all subsequent analyses. Genetic diversity, FST, and Ne analyses were completed both including and excluding global outlier loci—while there was little difference between results including or excluding outlier loci for genetic diversity and Ne, the magnitude of FST was greater with outlier loci included, and the conclusion changed in one case for FST. Thus, we have included only results for neutral loci here for these two metrics.Global outlier loci (loci putatively under selection) were detected using PCAdapt  and Ne were reduced over time in southern populations, genetic diversity estimates were obtained using the populations model of stacks, and per‐generation Ne (5‐ to 7‐year generation time) was estimated using the linkage disequilibrium method in NeEstimator v2.01  and that putatively selected loci would be associated with relevant biological processes, analyses to determine outlier loci were conducted with PCAdapt using the method described above. We chose to use PCadapt instead of other programs for outlier detection for two reasons. First, only two “populations” were sampled, and the authors of OutFlank do not recommend its use in these situations  within the last 5–20 years Table , but the3.23.2.1R2 adj = 0.418, F27, 1,486 = 41.24, p < .001; mass R2 adj = 0.3907, F27, 1,481 = 36.81). Mean TL and mass decreased significantly for both sexes between 2002/2003 and each of 2015, 2016, and 2017 in the southern rivers (TL 7%–21% and mass 22%–47% reductions), except for Perch River males in two contrasts and Chalifour females in two contrasts. While there was no significant change between 2002/2003 and each of 2016 and 2017 years for females in Chalifour, the trend in decline remained clear  <1.1, suggesting convergence on a common posterior mode   between Perch and Icon in 2002/2003  than between Icon–Perch F and Chalifour F (0) or Chalifour M and F (3).Our prediction that signatures of selection would be present between historic and contemporary timepoints within southern rivers but not the northern river, with putatively selected loci related to growth, body size, and/or maturation, was supported. Eleven to 263 loci were outliers (0.17%–2.83%) depending on the scenario tested Figure . OutlierSex‐specific analyses provided greater resolution than with sexes combined Figures . For exaF (no outliers were found for Icon–Perch M or Takwa) Rivers. Southern F/M combined and M had no blast hits. Otherwise, between 2 and 6 alleles were annotated for each blast. Because annotations were completed against all mapped Metazoa, at level 2 go annotation, functional annotations included many different biological processes, molecular functions, and cellular components. Three relevant processes indicated were growth, metabolism, and developmental process (Table Blasts were conducted for southern (F/M combined and separately), Chalifour (F/M combined and separately), and Icon–Perch ss Table .4Our results suggest that nascent genetic changes associated with harvesting can arise in wild fish populations within a 1–2.5 generation period, a shorter timescale than previously observed in other fisheries. Concurrent with reductions in body size within a 15‐year period 2002/2003–2017)  between 2002/2003 and each of 2015–2017 within all southern rivers, except for in Perch River males Figure , 2007.ST within Chalifour and Perch Rivers between years and between Icon and Perch 2015 were small  over differing timescales and varying fishing pressures  . Using averages for 11‐year‐old walleye in the south for each 2002 (515 mm) and 2015 (424 mm) , R = −7 mm per year. Given realistic 2h estimates (0.3)  Law, , if obseLastly, alternative explanations for the nascent genomic change evident in Icon–Perch could also include sampling bias, spatial movement, or increased gene flow. If sampling bias was present, Perch 2003 individuals could have been from a different population, but 2002/03 samples were genetically indistinct within rivers  would likely have been muted, providing inaccurate information for fisheries managers.Our study illustrates the benefits of integrating life history and genomic methods for conservation in order to understand the factors affecting population change  am fortunate to have worked with the Cree Nation of Mistissini since 2000 when I started graduate studies in Louis Bernatchez’ Lab. I have a long‐standing interest in conservation biology and have long admired the incredible knowledge that Cree fishers have of the fish found on their traditional territories. Like many Indigenous groups in northern Canada, the Cree seek a balance between maintaining their own cultural traditions, protecting the environment for future generations, and developing economically, using the best available information. Owing to past colonialism, a framework that involves active collaborations with Indigenous peoples is essential for improving resource conservation in northern Canada and for deriving the full socio‐economic benefits of fisheries and other natural resources. The integration of IK and WSM, as two different but complementary ways of knowing, is a critical step toward fostering local resource management and empowering local communities to make effective resource conservation decisions.I (Ella) began working in the same system as Dylan in 2016 as a postdoc in his laboratory. My career goal is to work in areas related to biodiversity conservation, and I believe strongly that any conservation efforts that biologists are involved in should be in concert with stewards of the land. Stewards include Indigenous groups with a long history on the land, or also other hunters, fishers, or farmers who have a long history using a given resource. In ecology, understanding results is often very rooted in recognizing the idiosyncrasies of a system, which stewards often know better than scientists. I did not learn how to weave knowledge types during my earlier training, and the ability to work with the Cree Nation of Mistissini and learn how to interweave IK with WSM toward conservation was a central motivation for my wanting to join Dylan’s lab.In my (Pamela) academic and work experience thus far, one of the perspectives I recognized and was able to relate in some way was the unique knowledge and connection Indigenous people have to the environment. For hundreds of years, their survival depended on a harmonious relationship with their surrounding land, water, wildlife, etc. The Cree skills gained have been passed on from one generation to another, and in most cases, conservation measures are created for the purpose of continuing to transfer this knowledge. Being raised in my Cree community of Mistissini, and working in the field of environment for the past six years, has allowed me to understand the expertise our land users and community members have because of this established relationship. I believe the use of Indigenous knowledge and Western science methods allows for a more detailed understanding of the research being studied, though further work needs to be done to define how the two knowledge types are or can be applied. These efforts are currently ongoing with the fish studies we (in Mistissini) have conducted with Concordia University over the years. It is my objective to ensure the existing Indigenous knowledge, more specifically the knowledge from the Cree people of Mistissini, is respected and incorporated in research and decision‐making regarding environmental management.The authors declare no competing interests.Supplementary MaterialClick here for additional data file.


Mexican hand tree or Canac (Chiranthodendron pentadactylon) is a temperate tree species of cloud and pine-oak forests of southern Mexico and Guatemala. Its characteristic hand-shaped flower is used in folk medicine and has constituted the iconic symbol of the Sociedad Botánica de México since 1940. Here, the evolutionary history of this species was estimated through phylogeographic analyses of nuclear DNA sequences obtained through restriction site associated DNA sequencing and ecological niche modeling. Total genomic DNA was extracted from leaf samples obtained from a representative number (5 to 10 per sampling site) of individuals distributed along the species geographic range. In Mexico, population is comprised by spatially isolated individuals which may follow the trends of cloud forest fragmentation. By contrast, in Guatemala Chiranthodendron may constitute a canopy dominant species near the Acatenango volcano. The distributional range of this species encompasses geographic provinces separated by the Isthmus of Tehuantepec.The The objectives of the study were to: (i) estimate its genetic structure to define whether the observed range disjunction exerted by the Isthmus of Tehuantepec translates into separate populations, (ii) link population divergence timing and demographic trends to historical climate change, and (iii) test hypotheses related to Pleistocene refugia.Patterns of genetic diversity indicated high levels of genetic differentiation between populations separated by the Isthmus. The western and eastern population diverged approximately 0.873 Million years ago (Ma). Demographic analyses supported a simultaneous split from an ancestral population and rapid expansion from a small stock approximately 0.2 Ma corresponding to a glacial period. The populations have remained stable since the LIG (130 Kilo years ago (Ka)). Species distribution modelling (SDM) predicted a decrease in potential distribution in the Last Interglacial (LIG) and an increase during the Last Glacial Maximum (LGM) (22 Ka), Mid-Holocene (6 Ka) and present times.Divergence time estimations support the hypothesis that populations represent Quaternary relict elements of a species with broader and northernmost distribution. Pleistocene climatic shifts exerted major influence on the distribution of populations allowing dispersion during episodes of suitable climatic conditions and structuring during the first interglacial with a time period length of 100 Kilo years (Kyr) and the vicariant influence of the Isthmus. Limited demographic expansion and population connectivity during the LGM supports the moist forest hypothesis model. Chiranthodendron pentadactylon Sessé ex. Larreat is an evergreen temperate tree species of tropical montane cloud forests and pine-oak forests of southern Mexico [Mexican hand tree or tree of the little hands in Mexico and Canac (hand-flower) in Guatemala. The flowers are currently used in folk medicine to treat heart conditions, high pressure [Sociedad Botánica de México since the early 40s. In Mexico, the population spatial structure is constituted by spatially isolated individuals which may follow the trends of cloud forest fragmentation. On the other hand, Véliz [C. pentadactylon represents a canopy dominant species of the cloud forest community found near the Acatenango volcano in Guatemala.n Mexico   [C. pentadactylon as threatened. This implies that populations could become endangered in the short or medium term if the factors that negatively affect their viability continue to operate including deterioration or modification of their habitat or direct reduction of their population sizes [In the IUCN Red List of Threatened Species , C. pentuatemala . The NorAT-2010)  however on sizes .Chiranthodendron Larreat. along with Fremontodendron Coville, form the Fremontodendreae tribe within the Bombacoideae subfamily of the Malvaceae family. Fremontodendron bears three species: F. californicum (Torrey) Coville, F. mexicanum Davidson and F. decumbens R. M. Lloyd. They are shrubs and small trees that constitute distinctive elements of the chaparral vegetation in the Sierra Nevada foothills and coastal ranges of California extending to scattered locations in central and western Arizona and northern Baja California in Mexico [Chiranthodendron and Fremontodendron share leaf-opposed hermaphroditic flowers greater than 2 cm in diameter and the production of large amounts of nectar [The monospecific genus n Mexico . Chirantf nectar .The high biotic diversity of Mesoamerican forests , 10 is tChiranthodendron-Fremontodendron potential predecessors from the early Lutetian. Hence, species with north temperate affinity constitute forms that survived the progressive drying and cooling trends of the middle Eocene and early Miocene. Subsequent colonization events have ensued during the Pliocene epoch (5.33–2.59 Ma) whence the cooling trend subsided gradually culminating with higher temperatures and wetter climatic conditions in the mid-Pliocene (3.6 Ma). Thereupon, during the late Pliocene (3 Ma) temperatures decreased leading to the onset of the Pleistocene (2.59–0.01 Ma) glacial cycles with the formation of the North American Laurentide sheet approximately 2.6 Ma [The drying trend is evident from pollen records suggesting the last appearance of y 2.6 Ma . These hy 2.6 Ma –22. Specy 2.6 Ma . The extThe genetic and demographic consequences suggested for Mesoamerican cloud forest species have been interpreted under refugia hypotheses, which describe differing precipitation regimes. These include the moist forest hypothesis and the dry refugia model. The moist forest hypothesis states that during glacial periods there was no significant change in precipitation allowing the development of population connectivity, downslope migration and range expansion . The degChiranthodendron covers several geographic provinces separated mainly by the Isthmus of Tehuantepec and may represent a potential physical and ecological barrier [Presently, Mesoamerican cloud forests take place in narrow altitudinal zones  and occu barrier  to dispe barrier  which maC. pentadactylon present distribution, the evolutionary history is examined through phylogeographic, population genetic and ecological niche modelling approaches. The main objectives of the study were to use C. pentadactylon to: (i) estimate the genetic structure to define whether the observed range disjunction exerted by the Isthmus of Tehuantepec translates into separate populations, (ii) link population divergence timing and demographic trends to historical climate change, and (iii) test hypotheses related to Pleistocene refugia.To gain insight into the potential historical factors influencing Genetic analyses were conducted using nuclear loci obtained through restriction-site associated DNA sequencing (RADSeq). Nuclear genomic DNA may be the source of numerous unlinked loci of enough resolution to detect spatial distributional patterns of gene genealogies . MoreoveST) of 0.62879 followed by moderate levels of within population variation (37.12%). The estimated degree of genetic differentiation among groups separated west and east of the Isthmus supports their attribution as separate populations referred to as western and eastern population respectively.The overall nucleotide diversity (Pi) was low 0.01463). The STRUCTURE analysis yielded a K value of 2 for the number of groups  for the replicate runs displays a good model performance (0.970). The species distribution modelling (SDM) for the LIG shows a major reduction in the species ecological niche as compared with the SDM for the LGM and Mid-HLC in which the species ecological niche is increased. The potential geographic distribution is maintained in the LGM through the Mid-HLC but is further increased in recent times Fig. .Fig. 6CC. pentadactylon encompasses geographic provinces separated by the Isthmus of Tehuantepec. The Isthmus of Tehuantepec is a savannah-like valley area [Palicourea padifolia [Rhipsalis baccifera which followed the trends of cloud forest demographic dynamics during periods of climate change [Podocarpus matudae and Liquidambar styraciflua, the shrub P. padifolia, the herb Moussonia deppeana and the epiphytic Rhipsalis baccifera as well as the rodent species Peromyscus aztecus, Reithrodontomys sumichrasti, and Habromys lophurus, the hummingbird species Amazilia cyanocephala, Campylopterus curvipennis and Lampornis amethystinus, the woodcreeper Lepidocolaptes affinis and the passerine species Chlorospingus opthtalmicus, Buarremon brunneinucha and Basileuterus belli [Psittachanthus schiedeanus [The distributional range of ley area  of high ley area . Geologiley area , 33. Theadifolia  and of te change  revealedus belli  likewiseiedeanus  the vicaC. pentadactylon lineages distributed west and east of the Isthmus of Tehuantepec and were thenceforth considered as separate populations. The degree of genetic differentiation among populations was further estimated by the global AMOVA implemented by Arlequin which indicated high levels of genetic differentiation among populations and moderate levels of within population variation. The high vagility of the pollination vectors such as birds and bats might induce low levels of among population variation. Nevertheless, the probability of long-distance dispersal events along the Isthmus is reduced given the hermaphroditic floral morphology and therein breeding system. On the other hand, the dichogamous nature of the flowers promotes a mixed-mating mechanism which derives in moderate levels of within population genetic variation. Further, low levels of within population subdivision are expected given the highly vagile pollination vectors such as birds and bats since they are likely to visit numerous plants [To determine whether the distribution disjunction exerted by the Isthmus of Tehuantepec represents a biogeographical barrier to dispersal and gene flow, population estimates were conducted based on nuclear data derived from RAD sequencing. The degree of population substructure was estimated under the Bayesian approach implemented by the software STRUCTURE. The Bayesian algorithm detected a genetic differentiation among s plants . Seed diFinally, the relationships among individuals estimated by the Neighbor-Net algorithm consisted on the two populations detected by previous analyses. Moreover, the StarBEAST2 tree showed a strong support for the differentiation of the populations.C. pentadactylon might have been influenced by the climatic oscillations of the Quaternary ice ages. To relate genetic divergence to pre-Pleistocene and Pleistocene events, calibrated time trees were calculated under the multispecies coalescent model implemented in StarBEAST2. Chiranthodendron and its sister genus Fremontodendron bring together the Fremontodendreae tribe within the Bombacoideae subfamily. These might have derived from predecessors with Laurasian origin [Chiranthodendron and contracted its range to the highlands where suitable climatic conditions remained. The DIYABC analysis based on SNPs sequences supported a simultaneous split from an ancestral population scenario. This scenario suggests a once widespread ancestral species that contracted its range during a period of unsuitable climatic conditions as those inferred for the last 800 Kyr leading to variation in population continuity and isolation. Range contraction might have included a northernmost distribution. This is supported by the upheld distribution of its sister genus Fremontodendron in southwestern United States and northwestern Mexico. This genus is comprised by shrubs and small trees of chaparral communities [Changes in the distribution of cloud forests throughout time have been determined by factors such as geological events and climate change. In addition to the occurrence of the Isthmus of Tehuantepec, the geographic range of n origin  which min origin . Accordin origin , the MRCn origin . The extmunities  and dry munities . Some prmunities . Later, munities  and the munities .Changes in population size over time were estimated through BSPs based on SNPs sequences. These analyses detected ongoing increases in effective population size from 0.5 Ma onwards followed by sudden demographic expansions. The latest demographic expansions might coincide with a glacial period dated approximately 0.2 Ma . These eP. padifolia [Podocarpus spp., distributed in Mesoamerica along with the reconstruction of potential distributions during the LIG and LGM [L. styraciflua [R. baccifera [P. schiedeanus [Podocarpus spp. [Phylogeographic studies on additional cloud forest species allowed the recognition of signatures of rapid demographic expansion. For instance, haplotype diversity and topology estimations coupled with neutrality tests suggested a rapid increase in population size from a small stock in the distylous shrub adifolia . Howeveradifolia  during t and LGM  allowed raciflua , R. baccaccifera , P. schiiedeanus  and Podopus spp.  of whichC. pentadactylon, reduction in potential distribution range predicted for the LIG may have prevented further demographic expansions but nevertheless reductions in effective population sizes were not observed. The latter suggests that populations might have survived in interglacial refugia and were able to maintain their effective population sizes. The absence of demographic expansions predicted for the LGM coincides with the demographic trends expected under the moist forest hypothesis.In The populations have remained constant from the LGM to present times even at the onset of an increase in potential distribution, suggesting the influence of additional variables such as ecological and anthropic factors.C. pentadactylon a species with limited adaptability to recent climate change and global warming.The phylogeographic approach conducted allowed the recognition and attribution of the Isthmus of Tehuantepec as a current driver of population differentiation and of the climatic oscillations of the Pleistocene epoch as a determining factor for their current distribution. Demographic analyses and divergence timing estimation suggest that populations derived from an ancestral population possibly of more widespread and northernmost distribution that underwent range contraction around the onset of the first interglacial with a time period length of 100 Kyr (800 Ka). Estimation of changes in population size over time suggests a demographic expansion during the glacial period prior to the LIG. The genetic diversity measures suggest an expansion from a small size population. The SDMs predicted a reduction in potential distribution for the LIG. However, population size reductions were not detected. Populations have not undergone demographic expansions since the unsuitable climatic conditions of the LIG and appear to remain stable. Nevertheless, the low genetic nucleotide diversity, low effective population sizes and restricted distribution to specific biomes limited in spatial range, make Norma Oficial Mexicana (NOM-059-SEMARNAT-2010), could render it endangered and consequently at risk of extinction. The disjunct distribution between Chiranthodendron and its sister genus Fremontodendron as well as the recent divergence time estimated for the extant populations, suggest that it represents a relict species and thus bears an additional value for conservation.Furthermore, the reduction of forest areas due to anthropic influence as established by the IUCN and the C. pentadactylon provides to forest ecosystems, and to determine the characters subject to selection. This information may provide useful insights into the reproductive requirements and success of the species to efficiently conduct conservation efforts.Additional ecological and evolutionary studies are required to determine the impact that Chiranthodendron pentadactylon is a tree of up to 30 m tall , the Instituto de Ecología AC at Pátzcuaro, the Facultad de Agronomía de la Universidad de San Carlos de Guatemala (AGUAT), the Escuela de Biología, USAC (Herbario BIGU), the Missouri Botanical Garden (MO) and the Chicago Natural History Museum. Each later defined population has an accompanying voucher deposited at the Herbarium UAA . Samples were pooled into a multiplexed library and sequenced on an Ilumina NextSeq500 platform to generate 150-bp single-end readings.Total genomic DNA was extracted following the cetyltrimethylammonium bromide (CTAB) protocol  with an The raw sequence data were analyzed and assembled de novo in the software pipeline ipyrad v0.7.28 , which iWhen clustered across samples a minimum number of samples per locus were set to 66 to maximize the representativeness of the total samples per locus. The samples had an average of 565 K reads that passed quality filtering. These clustered into an average of 8837 clusters per sample with a mean depth of 4526 producing a mean of 4075 consensus sequences per sample and a maximum total of 70 loci were recovered  measure proposed by Nei (1987) and implemented by the software DnaSP v6 . The estThe underlying degree of genetic structure was determined through the Bayesian clustering approach implemented by the software STRUCTURE v2.3.4 . The subGenetic structure was further evaluated through a global analysis of molecular variance (AMOVA) using the software Arlequin v3.5 . The anaTo visualize the phylogenetic relationships among and within populations, a phylogenetic network was constructed using the Neighbor-Net algorithm implemented by the software SplitsTree5 . The relC. pentadactylon. This calibration point derives from a dated phylogeny for the Malvaceae family, which was used to infer divergence dates and diversification rates within the Theobroma genus [C. pentadactylon and its sister genus Fremontodendron was on the order of 5 Ma. This was set as the median age for the informative lognormal prior with a standard deviation of 0.01. The MCMC chain length was 180,000,000 and logged every 5000. The log files were analyzed with Tracer v1.7.1 for parameter convergence. The burn-in was set to remove 10 % of the tree files before the generation of a maximum clade credibility tree with median heights in TreeAnnotator.To relate the genetic divergence among populations to pre-Pleistocene and Pleistocene events, calibrated time trees were calculated under the multispecies coalescent model implemented in StarBEAST2 . StarBEAma genus . The resTo assess changes in population size over time and determine their correspondence to pre-Pleistocene or Pleistocene events, a Coalescent Bayesian Skyline Plot (BSP) was estimated for each group defined in STRUCTURE and later defined as separate populations, using BEAST v.2.5.2. Linked SNPs data were set as input files. The best substitution model for each set of SNPs was determined using jModelTest through the implementation of the AIC Table . The corC. pentadactylon was inferred from an approximate Bayesian computation (ABC) in which evolutionary scenarios were simulated and compared through posterior probabilities using the DIYABC v2.1.0 [The population history of C v2.1.0  softwarePosterior probabilities of scenarios were assessed using a polychotomic weighted logistic regression on 1% of the simulated datasets. The fit between the simulated and observed datasets was evaluated through the implementation of a model checking procedure based on a principal component analysis (PCA). Confidence in scenario choice was assessed by means of the simulation of 500 pseudo-observed datasets (PODs) under each scenario to estimate Type I and Type II error rates.C. pentadactylon for the present day, Mid-Holocene , Last Glacial Maximum  and Last Interglacial  was predicted using Maxent 3.4.1 [Chiranthodendron pentadactylon Larreat in GBIF Secretariat (2019). GBIF Backbone Taxonomy. Checklist dataset https://doi.org/10.15468/39omei), TROPICOS  and REMIB (http://www.conabio.gob.mx/remib/doctos/remib_esp.html) databases and represented 152 unique localities after data cleansing including the removal of duplicate points. The models were built from 9 climate layers selected through the jackknife method. These had a 2.5 arc minute spatial resolution and were acquired from the WorldClim database [The potential distribution of nt 3.4.1 . The geodatabase . Layers Additional file 1. Taxon sampling, geographic location and voucher information. The two specimens collected as vouchers are deposited in the herbarium of the Universidad Autónoma de Aguascalientes (HUAA).Additional file 2. RADSeq de novo assembly stats of raw sequences.Additional file 3. Sequence matrix of 36 polymorphic nuclear loci.Additional file 4. Nuclear loci and SNPs data sets substitution models.Additional file 5. Evanno method results from STRUCTURE HARVESTER.


Oreocharis benthamii in allopatry and sympatry based on ISSR data for 754 individuals from 26 populations, in order to understand the processes leading to speciation. Contrary to expectations, the facultative xenogamy (mixed mating) species O. benthamii has a relatively low genetic diversity within populations  and high genetic differentiation among populations , as is typically found for selfing species. Genetic variance between the two varieties in sympatric populations  is significantly more than that in allopatric populations . Consistent with the taxonomical delimitation of the two varieties, all sampled individuals of O. benthamii clustered into two genetic groups. Moreover, the genetic structures of populations of both varieties are correlated with their different geographical origins. Our studies show that significant divergence between sympatric populations of the two varieties could be attributed primarily to reinforcement by genetic divergent selection in sympatry where secondary contact had occurred. The major proportion of the genetic variation in outcrossing and mixed mating plants may exist among populations when the populations are distributed in fragmented habitats, due to the paucity of suitable habitat combined with inefficient seed dispersal mechanism and limited pollinator foraging area that may limit the gene flow.The pattern of genetic differentiation between diverging species receives much attention as one of the key observable features of speciation. It has often been suggested that introgression between closely related species occurs commonly where their distributions overlap, leading to their becoming more morphologically and genetically similar, but there are a few opposite results. However, most of these studies have been carried out with animals and separate species; few have looked at intraspecific cases, especially in plants. Here, we conduct a comparative study on patterns of genetic differentiation among populations of two varieties of  Oreocharis benthamii in sympatric populations is significantly more than that in allopatric populations.Introgression between closely related species occurs commonly where their distributions overlap, leading to their becoming more morphologically and genetically similar. However, few of these studies have looked at intraspecific cases, especially in plants. Here, we report a reverse situation that the genetic variance between two varieties of  Genetic differentiation or speciation has mainly occurred during periods when habitats were fragmented and isolated , and its lateral veins and reticulate veinlets are more prominent than those of var. benthamii  boundaries. The ISSR (inter simple sequence repeat) is an easy handling, good reproducibility, low cost, quick and highly informative technique, and widely used for plant population genetic studies  How genetic diversity and genetic differentiation are distributed throughout all populations of the species; (2) whether there is increased or reduced genetic differentiation between sympatric populations compared with allopatric populations of these two varieties.Plants of s Figure . The minn Figure ‐4 and the Figure ‐4. The te Figure . Sympatr22.1O. benthamii var. benthamii and var. reticulata are nonclonal perennial acaulescent herbs endemic to China, and their distribution ranges are partially overlapped, mainly in southern China  and allopatric  .Both n Figure . In this) Figure , to inve) Figure . Samples2.22, 0.7 mM dNTPs, 2.0 μM primer, 2.0 units of Taq polymerase, and 30 ng of template DNA and double‐distilled water. Polymerase chain reactions (PCRs) amplification was conducted on a Bio‐Rad T100™ Thermal Cycler (Bio‐Rad) under the following conditions: initial denaturation at 94°C for 5 min, followed by 39 cycles of 30 s at 94°C, 45 s at a primer‐specific annealing temperature, extension for 90 s at 72°C, and a 10‐min final extension step at 72°C. The annealing temperature for each primer is given in Table Total genomic DNA was extracted from silica‐dried leaf material using a modified cetyl trimethyl ammonium bromide (CTAB) procedure , number of effective alleles (Ne), percentage of polymorphic loci (PPL), Nei's genetic diversity (H), and Shannon's information index (I). At the species level, three genetic diversity measures /HT)), the level of gene flow (Nm), and the genetic distance between populations were also computed using the model presented in Nei  and converted into a binary data matrix. The resulting presence/absence data matrix was analyzed using POPGENE version 1.32  tree based on Nei's genetic distance with the program NEIGHBOR incorporated in the software package PHYLIP version 3.6 , from K = 1 to 26. The maximum number of clusters used was greater than the number of populations in order to detect possible substructuring within the samples. All runs were performed with the admixture model without prior population information, assuming correlated allele frequencies among populations, with burn‐in and run lengths of 100,000 and 1,000,000 iterations, respectively. The optimal number of clusters (K) was determined following the guidelines from Wang   polymorphic ISSR bands, of which 435 (95.81%) and 323 (71.15%) polymorphic bands were identified in the populations of var. reticulata and var. benthamii, respectively. Of the 454 bands, 131 (28.54%) were found only in the populations of var. reticulata and 19 (4.19%) were present only in var. benthamii. The populations of the species showed an overall Shannon diversity index (I) of 0.3822. Shannon's diversity index of var. reticulata (I = 0.3698) was greater than that of var. benthamii (I = 0.2977). At the population level, the percentage of polymorphic loci (PPL) and Shannon's diversity index (I) of the species was, respectively, 30.34% and 0.1528 on average. The average level of genetic diversity of var. reticulata populations  was significantly higher than that of var. benthamii . Populations SDH3 (var. reticulata) and DXTS3 (var. benthamii) showed the highest levels of genetic diversity , while populations SQY  and DBX  exhibited the lowest levels.Values obtained for ISSR polymorphism and genetic diversity are summarized in Table 3.2O. benthamii are presented in Table GST for all populations of the species was estimated as 0.5867, indicating that 58.67% of the genetic variability was distributed among populations, and the estimate of gene flow (Nm) per generation among populations was 0.3522. Genetic differentiation among populations in var. reticulata (GST = 0.5394) was slightly lower than that in var. benthamii (GST = 0.5614); accordingly, the mean estimated gene flow among populations in var. reticulata (Nm = 0.4269) is a little higher than that in var. benthamii (Nm = 0.3906). The AMOVA analysis (Table ST = 0.659) of the total variation in the species was partitioned among populations, and the variances among populations in var. reticulata  and var. benthamii  were almost the same. Of the total molecular variance, 16% was attributable to the divergence between var. reticulata and var. benthamii, 53% to population differences within varieties, and 31% to individual differences within populations  among sympatric populations was almost the same as that  among allopatric populations . In addition, the variance  between the two varieties in sympatric populations was significantly more than that  in allopatric populations . In addition, there was no correlation between genetic and geographical distances among all sample populations of O. benthamii from the sympatric region (Xiangtou Mountain) . However, there was a weak or moderate relationship among populations within var. reticulata  or var. benthamii .The Mantel test Figure  revealed3.3K = 2 and assigned all populations of the species to one of two genetic clusters based on allele frequencies  and two populations of var. benthamii , which suggests a higher level of admixture of the two gene pools within the four populations. With K = 15 (the best K based on Parsimony Index) and 17 , about half of the populations of both varieties were assigned to independent genetic clusters, and some geographically close populations were placed into the same genetic clusters  (highlighted green) and cluster II (var. benthamii) (highlighted red). Cluster I further formed two groups with three well‐resolved clades . One group consisted of two clades (A and B), and the other group consisted only of clade C, which comprised all populations of var. reticulata from northern Guangdong. Clade A comprised all populations of var. reticulata from western Guangdong and Guangxi, whereas clade B included all populations from eastern and central Guangdong. Cluster II also further formed two well‐resolved clades . Clade D comprised all populations of var. benthamii from central and northeast Guangdong and Fujian, and clade E consisted of all populations from southeast Guangdong. An unrooted neighbor‐joining (NJ) tree based on Nei's genetic distance also separated all sampled individuals into two clusters in accordance with the morphological delimitation between var. reticulata (highlighted green) and var. benthamii (highlighted red) , a result different from that in the UPGMA dendrogram. The var. benthamii cluster formed two groups with three well‐resolved branches. One group consisted only of population DFX from northeast Guangdong, and the other group consisted of two branches, population DNJ from Fujian and another clade including all populations from eastern and central Guangdong. The STRUCTURE analysis  Figure . The NJ reticulata (ringed in green) and var. benthamii (red). The var. reticulata group was divided into three subsets, which comprised all populations from, respectively, eastern and central Guangdong, northern Guangdong, and western Guangdong and Guangxi. There were also three subsets in the var. benthamii group: DFX, DNJ, and the subset from eastern and central Guangdong. The result of PCoA analysis thus confirmed the partitioning results obtained from UPGMA clustering and the NJ tree, especially the latter.The PCoA analysis Figure  shows tw44.1O. benthamii, whether at the species or at the variety level, has a very low level of population genetic diversity and a high level of population differentiation, but a high level of species and variety genetic diversity.Outcrossing species would be expected to have higher within‐population genetic diversity and lower population differentiation values than selfing species , which was <1, for O. benthamii suggested that gene flow between populations of O. benthamii was limited by the extent of pollen and seed dispersal and was insufficient to counter the effects of random drift  plants may exist among populations, rather than within populations, when the plants are distributed in fragmented habitats, due to the paucity of suitable habitat combined with inefficient seed dispersal mechanism  also detected two gene pools (var. reticulata and var. benthamii) for all populations of O. benthamii, confirming the partitioning results revealed by UPGMA clustering and the NJ tree. All these approaches demonstrated that O. benthamii could be differentiated into two distinct varieties. There were different admixtures within individuals in all populations except for two populations (SDHS2 and SXMS) of var. reticulata from west Guangdong and Guangxi and one population (DBX) of var. benthamii from eastern Guangdong. Admixed individuals, reflecting introgression, were detected in both directions, and the gene flow between the two gene pools (var. reticulata and var. benthamii) was significantly asymmetric in most populations. The small amount of admixture within individuals of most populations probably arose from gene flow between var. reticulata and var. benthamii in processes associated with recent migration in the regions of overlap as well as earlier introgression.The results of both NJ analysis and UPGMA clustering of all individuals sampled from 4.3reticulata and var. benthamii. The results presented here show that differentiation among populations of O. benthamii in the allopatric region  is similar to that in the sympatric region . However, the variance between the two varieties in sympatric populations  is significantly greater than that in allopatric populations . This indicates that the degree of differentiation between the two varieties in the sympatric region is significantly higher than that in the allopatric region. A high level of differentiation between species in sympatry or parapatry may arise from demographic processes associated with range expansions by the two species  made between allopatric and sympatric populations of var. reticulata, but not those of var. benthamii  were yellow‐green  leading to the increased genetic divergence observed in sympatry. However, a more extensive survey combining morphological, ecological, and genomic data could make it possible to reconstruct the phylogeographic history of O. benthamii in order to test this hypothesis.Selection may increase ecological adaptation to different habitats, resulting in a decrease in interspecific competition in sympatry or parapatry Nosil, . Our fiee Figure ‐3,b‐3, bn Figure ‐4, that n Figure . Charactn Figure . Reinforn Figure . During n Figure . When ren Figure . This din Figure . We suggNone declared.Qiong Fu: Conceptualization (supporting); data curation (supporting); formal analysis (supporting); investigation (supporting); methodology ; project administration (supporting); software ; validation (supporting); visualization ; writing – original draft ; writing – review & editing . Guo‐Hui Lu: Investigation (supporting). Yu‐Hui Fu: Investigation (supporting). Ying‐Qiang Wang: Conceptualization (lead); data curation (lead); formal analysis (lead); funding acquisition (lead); investigation (lead); methodology (lead); project administration (lead); resources (lead); software (lead); supervision (lead); validation (lead); visualization (lead); writing – original draft (lead); writing – review & editing (lead).Supplementary MaterialClick here for additional data file.


Arabidopsis thaliana, which share a common recurrent parent (Col-0). Using a genotype-by-sequencing approach (GBS), we identified single nucleotide polymorphisms  and subsequently built updated linkage maps in each of the 14 RIL sets. Simulations in individual RIL populations indicate that our GBS markers have improved power to detect small effect QTL and enhanced resolution of QTL support intervals in comparison to original linkage maps. Using these robust linkage maps, we imputed a common set of publicly available parental SNPs into each RIL linkage map, generating overlapping markers across all populations. Though ultimately depending on allele frequencies at causal loci, simulations of the NAM panel suggest that surveying between 4 to 7 of the 14 RIL populations provides high resolution of the genetic architecture of complex traits, relative to a single mapping population.Linkage and association mapping populations are crucial public resources that facilitate the characterization of trait genetic architecture in natural and agricultural systems. We define a large nested association mapping panel (NAM) from 14 publicly available recombinant inbred line populations (RILs) of  Linkagee.g., maize, soybean, rice, etc.), and have been integral to the genetic characterization of important agricultural traits  and fundamental evolutionary mechanisms , numerous segregating populations founded by a broad array of accessions, and translational relevance to agro-ecologically important members of the Brassicaceae family . The NAM design has been implemented in A. thaliana using three RIL populations (Arabidopsis NAM design by utilizing 14 publicly available RIL populations that result from crosses between the recurrent Columbia accession (Col-0) and fourteen alternate founders (http://publiclines.versailles.inra.fr). We utilize a genotyping-by-sequencing (GBS) approach to augment existing marker genotyping and linkage maps in each RIL population, improving linkage mapping resolution for individual populations. Additionally, we impute an overlapping set of single nucleotide polymorphisms (SNPs) from all parental accessions  that utilize Col-0 as a common recurrent parent  approach to SNP discovery. We obtained DNA samples from Versailles, and used GBS methodologies slightly modified from those detailed in EcoRI and HindIII and then ligated customized adapters to each fragment containing the Illumina adaptor sequences and 8-10 bp barcode sequences. We substituted HindIII  in combination with EcoRI for the commonly used MseI 4-base cutter . Initial GBS libraries were sent to the RTSF Genomics Core  and follow-up runs were sent to the Genomic Sequencing and Analysis Facility . At both facilities, libraries were sequenced on the Illumina HiSeq 2500 platform (1 × 100 bp) and over 1 billion reads were assigned to barcoded samples.We selected 14 t parent . From eaA. thaliana reference genome (TAIR10) using two separate approaches and resulting SNPs calls were merged. First, we used SOAP  in order to set priors on genotype calls based on the probability of expected homozygosity in an F8 RIL population. Second, we utilized BWA’s aln and samse algorithms (ver. 0.7) to map reads to the TAIR10 reference. We then called SNPs using SAMtools mpileup and BCFtools view (ver. 0.1.19) algorithms. In both approaches, we retained only uniquely mapping reads and only SNP genotype calls with a read depth of eight or more. We used custom perl scripts to combine SNP calling approaches, merging the novel SNPs from BWA/SAMtools into the SOAPsnp results. Finally, we merged SNPs originally genotyped from each RIL population  into our GBS approach after converting INRA SNPs to the TAIR10 coordinate system. We visually inspected each RIL population to confirm that Col-0 vs. alternate parental marker states were congruent between our GBS data and markers available at INRA; inconsistent lines were dropped. Additionally, lines with excessive heterozygosity or limited genotyping were dropped; in total 4.1% of lines were excluded bringing the final population to 2028 RILs  for each chromosome using a Kosambi mapping function . We then removed any imputed genotypes where multipoint marker data estimated genotype probabilities  were less than 99%.For each population, we combined our new GBS SNP markers with existing INRA markers and imported these data into the R/qtl package (function . We thenscanone procedure to identify each QTL (testing genome-wide significance following 1000 permutations) and recorded effect size and 1.5 LOD intervals of each QTL. We then dropped the new GBS markers from the dataset and repeated mapping of the simulated trait with the mapping procedure outlined above using only the original INRA markers. We recorded if the simulated QTL was detected in each population using just the INRA markers and, if so, the effect size and 1.5 LOD interval size.To explore how our GBS SNPs improve mapping resolution and efficiency in each RIL population, we ran 1000 simulations, in which small and large effect QTL (∼10% and 30% percent variance explained (PVE), respectively) were simulated at a randomly selected SNP in each RIL population following imputation. In each simulation run, we used the maximum likelihood algorithm in R/qtl’s Because our GBS markers rarely overlapped across populations, we used the robust linkage maps of each individual population to impute a common set of SNP markers across all 14 RIL sets. We utilized the publicly available 250K SNP Arabidopsis dataset for imputation , this fill in approach has an average imputation error rate of 0.0016%  and a maximal error rate of 1.93% . All 14 RIL populations were merged together based on imputed, overlapping SNPs and neighboring markers in perfect linkage with respect to both marker state and missing data were reduced to a single entry. These SNPs could be used to map trait genetic architecture via GWA style analyses that control for population structure .Using the final imputed SNP files of our merged NAM population, we also generated a joint-linkage map for all 14 populations. Because recombination events can only be detected between polymorphic SNPs, we selected SNPs for which at least 11 of the 14 alternate parents shared a SNP state and differed from the recurrent parent. SNPs in populations that were not polymorphic for a specific marker were encoded as missing data  and its genetic architecture. To broadly examine the ability of different combinations of the 14 Arabidopsis RIL populations in resolving QTL across a range of effect sizes, we simulated two QTL scenarios. First, we selected all markers where all alternate parental lines were identical and differed from the recurrent Columbia parental line . We randomly selected a SNP marker and simulated a QTL at this marker for all RILs in all 14 populations; we then created 13 additional datasets of this trait by progressively dropping a randomly selected RIL population. This process was repeated 1000 times for each of seven QTL effect sizes . Second, we selected markers that varied in only one of the 14 RIL populations to explore how power to detect a rare causal QTL in a single population was influenced by adding additional invariant populations (which would influence sample size and trait mean estimation). We followed a similar approach to that above by simulating QTL of seven effect sizes for a randomly selected marker and repeating this 1000 times for each PVE category. In this second simulation, PVE settings were consistent with those above; however, because only one population varied, target PVEs were only realized in the single segregating population. We again created 14 separate datasets by progressively dropping a randomly selected RIL population that was not polymorphic.The ability to identify and characterize segregating genetic variation in NAM analyses depends upon the QTL effect size, the degree of linkage between causal gene and adjacent markers, the frequency of each allele in the founding parental lines (and subsequently in the RIL progeny of that specific cross), and the overall sample size of RILs in each allelic class from which to estimate mean and standard error. Moreover, the cost-benefit relationship of phenotyping multiple RIL populations will vary given both the trait . Supplemental material available at figshare: https://doi.org/10.25387/g3.12683750.In addition to data within this manuscript, we present supplemental files via FigShare. Fig. S1 and Fig. S2 contain linkage map and LD plots of RILs and the NAM population, respectively. Table S1 contains sequences of custom adapters described in the methods. We have submitted all individual RIL linkage maps, imputed SNPs across all 14 NAM populations, and a joint-linkage map where at least 11 alternative parents share a common SNP state to the dryad repository . Combining our new GBS markers with the original markers developed at INRA (range: 74-90 markers), we estimated new linkage maps in each of the 14 populations resulting in an average marker spacing of 0.4 cM (range: 0.3-0.7 cM) and an average maximum spacing of 7.9 cM  on Chr 1 (donated by Col-0) combined with a homozygous null copy of HPA2 on Chr 5 (donated by Ita-0 or Cvi-0) results in recessive embryo lethality and lines with these allelic combinations were lost during RIL development (FOLT) present on Chr 4 and Chr 5 (TAD3) found on Chr 5 and Chr 1 ; i.e., beyond the ∼150 per population here) to capture additional recombination events while concomitantly improving power through more accurate estimation of genotype means.In simulations of small and large effect QTL  within each individual RIL family, the addition of our GBS markers reduced 1.5 LOD intervals by an average of 23.3% (range: 13.4–34.4%) and 56.6% (range: 40.4–63.3%), respectively . These sArabidopsis dataset  lines  can further QTL discovery by ensuring maximal phenotypic variation in traits of interest segregating in a specific mapping population. Researchers utilizing a subset of the full NAM panel could also benefit from selecting RIL sets derived from the most negatively and positively deviating parental lines for a trait of interest. Together with other advanced segregating progeny (


The genetic markers on mitochondria DNA (mtDNA) and Y-chromosome can be applied as a powerful tool in population genetics. We present a study to reveal the genetic background of Kyrgyz group, a Chinese ethnic group living in northwest China, and genetic polymorphisms of 60 loci on maternal inherited mtDNA and 24 loci on paternal inherited Y-chromosome short tandem repeats (Y-STRs) were investigated. The relationship between the two systems was tested, and the result indicated that they were statistically independent from each other. The genetic distances between Kyrgyz group and 11 reference populations for mtDNA, and 13 reference populations for Y-STRs were also calculated, respectively. The present results demonstrated that the Kyrgyz group was genetically closer to East Asian populations than European populations based on the mtDNA loci but the other way around for the Y-STRs. The genetic analyses could largely strengthen the understanding for the genetic background of the Kyrgyz group. Based on two types of autosomal markers, insertion/deletion (InDel) [As one of the populous countries in the world, China consists of 56 official ethnic groups, some of them, including the Uygur, Kazak, Uzbek, and Kyrgyz groups, live in northwest China . On the  (InDel)  and shor (InDel) , our pre (InDel) ,8. The marker system on mtDNA can be applied as a useful tool for individual identification, maternal lineage test, and ancestry inference in forensic applications ,10,11. Ihttps://yhrd.org), which contains a large number of Y-STR haplotypes from different populations all over the world, can be used as reference population data.Another marker system used in this study is Y-STRs, which contribute to plenty of Y chromosomal haplotypes for forensic applications, historical researches, and genealogical investigation of paternal relatives ,14. BaseThe purpose of the current study was to further understand the historical background of the Kyrgyz group and its paternal and maternal genetic relationships with various populations. We also conducted an independence test between the two marker systems in this study based on the method, an extension of contingency chi-square tests for linkage disequilibrium , as suggNm (Nm = 138) samples were detected by the mtDNA marker system, Ny (Ny = 241) male samples were detected by the Y-STR marker system, and Nj (Nj = 88) samples were detected by both of the two marker systems. This study was performed in accordance with the humane and ethical research principles approved by the ethical committee of Xi’an Jiaotong University Health Science Center, China. All the reference population data for mtDNA and Y-STRs were collected from previously published researches.To detect the mtDNA loci and Y-STRs, we collected the blood samples of unrelated healthy individuals from Kyrgyz group in the Kizilsu Kirghiz Autonomous Prefecture, in the northwest of the People’s Republic of China. ® ID-X software v 1.3 .We detected 60 mtDNA loci using a commercial kit named Expressmarker mtDNA-SNP 60 , which contained 58 mtDNA single nucleotide polymorphisms (SNPs) including nt152, nt709, nt1541, nt1719, nt1811, nt2706, nt3010, nt3348, nt3970, nt4216, nt4491, nt4833, nt4883, nt5178, nt5417, nt5442, nt5460, nt6446, nt7028, nt7196, nt7600, nt8020, nt8414, nt8584, nt8684, nt8697, nt8701, nt8793, nt8794, nt8964, nt9123, nt9477, nt9545, nt9698, nt9824, nt10310, nt10397, nt10398, nt10400, nt10873, nt11215, nt11251, nt11719, nt12372, nt12705, nt12811, nt13104, nt13928, nt14569, nt14668, nt15043, nt15784, nt16126, nt16129, nt16311, nt16316, nt16319, nt16362), an InDel locus , and a (CA)n locus (nt514-nt524). These 60 loci were separately amplified with three multiplex amplification panels in three independent 10ul volume systems according to the manufacturer’s instruction [™ 24Y Direct ID System  was applied to detect 24 Y-STRs, containing 23 overlapped loci with PowerPlex Y23 System  and DYS460 loci. Multiplex amplification was conducted in a 10ul volume system as descried in the manufacturer’s instruction [Another commercial kit, Microreadertruction . Twenty-2O was used as negative control.In this research, M4615  and 9947A  were used as control DNA in the genotyping of Y-STRs and mtDNA loci, respectively. And ddHm) and nucleotide diversity (NDm), are calculated by DnaSP version 5.0 [m) and discrimination power (DPm) are calculated by the formula (1) below [For mtDNA loci, the two forensic parameters, haplotype diversity  below .(1)RMPmy), haplotype diversity (HDy), and matching probability (MPy) for Y-STRs are measured using the following formulas (2), (3) and (4) [Gene diversity (GD and (4) :(2)GDy =Fst values, for 58 mtDNA SNPs except 9bp and (CA)n among Kyrgyz group and other reference populations were estimated by Arlequin version 3.0 [https://www.nevgen.org/). In addition, another value of genetic distance for 23 Y-STRs except DYS460, i.e. pairwise Rst values [https://yhrd.org/amova) based on YHRD database. Plots of neighbor-joining (NJ) tree and multidimensional scaling analysis (MDS) were drawn by MEGA version 6.06 (http://megasoftware.net/) and PASW STATISTICS version 18.0 (https://www.ibm.com/products/spss-statistics) based on pairwise Fst values for 58 mtDNA SNPs and pairwise Rst values for 23 Y-STRs. After aligning with the revised Cambridge Reference Sequence (rCRS) , the gension 3.0 . For Y-St values , were esR statistical software version 3.0.2 (https://www.r-project.org/). The 88 individuals detected by both systems were studied in this part. For each pair of individuals, the number of Y-STRs with the same genotypes was recorded as R function (fisher.test {stats}) for independence test between Y-STRs and mtDNA SNPs was performed based on the matrix formed by The test of independence between the two systems was conducted by act test  by R funm and DPm values calculated on the basis of the number of haplotypes were 0.0807 and 0.9193. In addition, the values of HDm and NDm were 0.9838 +/− 0.0035 and 0.1820 +/− 0.0929.Allele frequencies of 60 mtDNA loci in 138 Kyrgyz individuals are shown in y and MPy values for 24 Y-STRs in 241 individuals are listed in y values on 24 Y-STRs ranged from 0.2468 (DYS393) to 0.7653 (DYS389 II). A total of 152 haplotypes and 27 haplogroups were defined by the 24 Y-STRs, which contained 23 Y-STRs overlapped with PowerPlex Y23 System , respectively , which was mostly prevalent in European and South Asian populations, according to previously reported researches ,26,27. HFst values for 58 mtDNA SNPs were calculated between the Kyrgyz group and 11 reference populations . The paRst values for 23 Y-STRs indicated the genetic relationships of Kyrgyz group and 13 reference populations. These 13 reference populations included East Asian populations: Beijing Han [Rst values, the Kyrgyz group had the closest distances to the northwest Chinese populations, Qiemo Uygur (Rst = 0.0831) and Xinjiang Uygur (Rst = 0.0840), followed by the European populations with Rst ranging from 0.1177 to 0.1639, and then by other populations from East Asia . The Kyrgyz group was the farthest distant from the African Americans (Rst = 0.3591). The MDS and NJ tree were plotted based on Rst values, respectively. In the MDS plot , indicating that the two systems were mutually independent from each other. The contingency table of the two genetic marker systems containing 3828 distinct pairs of 88 individuals was listed in In this study, we analyzed the genetic diversities based on the maternal inherited 60 mtDNA loci and the paternal inherited 24 Y-STRs for the Kyrgyz group in China. The haplogroup distributions for mtDNA and Y-STRs indicated the different genetic backgrounds of Kyrgyz group in maternal and paternal lineages. Also, we found that the results of the genetic relationships of the Kyrgyz group and reference populations were not completely equivalent between maternal and paternal inheritances.Fst or Rst values are fundamental measures to indicate the genetic distances between populations for mtDNA and Y-STRs, respectively. In our previous studies [Fst values among the Kyrgyz group and reference populations based on autosomal 30 InDels and 21 STRs to explore their genetic relationships in autosomal inheritance. Those results showed that Kyrgyz group had close genetic relationships to the Kazak and Uygur groups, who also lived in Xinjiang province. Then, the MDS plot for pairwise Fst values based on these autosomal InDels revealed that the Kyrgyz group was distributed in the middle of the plot and between East Asian and European populations [Pairwise  studies ,4, we caFst for mtDNA loci and pairwise Rst for Y-STRs. The two sets of values indicated that the Kyrgyz group had the closest genetic relationships with the ethnic groups in northwest China (the closest to the Kazak group on mtDNA markers and the closest to the Uygur group on Y chromosome markers). Beyond that, the pairwise Fst values for mtDNA SNPs revealed that the Kyrgyz group was genetically closer to East Asian populations, in contrast to the results from pairwise Rst values for Y-STRs, which showed that Kyrgyz group was genetically closer to European populations.In this study, we collected the genotyping data of populations worldwide as the reference populations to calculate pairwise On the MDS plot for mtDNA a, the KyThe particular genetic structure of Kyrgyz group was related to its geographical location, historical background, and marriage customs. The Kyrgyz individuals collected by our study were from the Kizilsu Kirghiz Autonomous Prefecture in the northwest part of China, where the northern and western parts are bordered by Kyrgyzstan and Tajikistan, respectively. The area where the Kyrgyz group located was the route of the ancient Silk Road  and an iFrom the Han dynasty to the early Qing dynasty, the Kyrgyz people were active in the Yenisei River Basin . In 1702The Kyrgyz group adopts an outside-marriage system , which sThe Fisher’s exact tests indicated that the two genetic marker systems were mutually independent between mtDNA SNPs and Y-STRs. In fact, the Y chromosome DNA marker is inside the nucleus of the cell, whereas mtDNA is in the mitochondria outside the nucleus. Therefore, the two marker systems are generally considered as independent inheritances during the courses of maternal and paternal inheritances. As expected, there were no statistically significant correlations between the two marker systems in current study. Since independent inheritance is the premise for the joint application of two different marker systems, and mtDNA and Y chromosome genetic markers are always analyzed simultaneously in the field of population genetics ,55, we pThe obtained mtDNA haplogroups in this study accounted for over two thirds of the studied Kyrgyz individuals, which were also common in East Asian populations, whereas the observed Y-STR halogroups that were mainly prevalent in East Asia populations accounted for only a small fraction of a total of the obtained Y-STR haplogroups. In population genetic relationship analyses, the Kyrgyz group was genetically closer to East Asian populations than European populations based on the mtDNA marker system. However, the analyses using the Y chromosome marker system provided different results, indicating the potential differences between the maternal and paternal inheritances. In future study, more genotyping data of different genetic markers from the Kyrgyz group are needed to further reveal the genetic background of the Chinese Kyrgyz group and its genetic relationships with other populations.


Since then, additional outbreaks have been identified in several populations of ibex and other wild ungulate species throughout the country. Although the first epizootic outbreak in wildlife was attributed to the introduction of an infected herd of domestic goats, the origin and the cause of its persistence remain unclear. The main aims of this study are to understand (i) the number of Sarcoptes scabiei “strains” circulating in wild ruminant populations in Spain, and (ii) the molecular epidemiological relationships between S. scabiei and its hosts.In Spain, sarcoptic mange was first described in native wildlife in 1987 in Cazorla Natural ParkSarcoptes microsatellite markers were used to characterize the genetic structure of 266 mites obtained from skin scrapings of 121 mangy wild ruminants between 2011 and 2019 from 11 areas in Spain.Ten S. scabiei in the wild ruminant populations investigated. While two genetic clusters of S. scabiei were host- and geography-related, one cluster included multi-host mites deriving from geographically distant populations.Seventy-three different alleles and 37 private alleles were detected. The results of this study show the existence of three genetic strains of S. scabiei in wild ruminants in Spain indicates that the spreading and persistence of the parasite may be conditioned by host species community composition and the permissiveness of each host population/community to the circulation of individual “strains,” among other factors. Wildlife–livestock interactions and the role of human-driven introduction or trade of wild and domestic animals should be better investigated to prevent further spread of sarcoptic mange in as yet unaffected natural areas of the Iberian Peninsula.The molecular epidemiological study of The online version contains supplementary material available at 10.1186/s13071-021-04673-x. Sarcoptes scabiei affects more than 100 mammalian species worldwide, causing a highly contagious skin disease known as sarcoptic mange or scabies. Since it can result in significant declines in local wildlife populations, this disease has received particular attention in wildlife conservation and management for decades [The ubiquitous mite , causing a decline of nearly 95% in the local native population of Iberian ibex (Capra pyrenaica) over 4 years [Cervus elaphus) [Rupicapra pyrenaica parva) [Dama dama) [Capreolus capreolus) [Ovis aries musimon) [Ammotragus lervia) [In Spain, sarcoptic mange was first described in native free-ranging wild ruminants in late 1987 in the Cazorla Natural Park , causing 4 years . Since ta parva) , fallow musimon) , and the lervia) , in the  lervia) .S. scabiei relies on suitable hosts, a multi-host system can provide the parasite with higher opportunities to persist and spread [S. scabiei, such as red fox and Iberian wolf  [Sus scrofa). While foxes are scavengers and might represent only a marginal and weak transmission pattern of sarcoptic mange for wild cervids and bovids, top predators such as the Iberian wolf, which is currently present in Spain mostly in the northern region , might have prey–predator interactions with red and roe deer and, on rare occasions, with chamois [S. scabiei has been detected [Since the direct life cycle of d spread . Wild ructively)  and wild chamois , 14. Intdetected , and wilS. scabiei mites have failed to recognize host-specific differences [S. scabiei into species-specific variants [S. scabiei between raccoon dogs and Japanese serow with weak prey–predator interaction  has alsin Kenya . All theral Park , where t changes . This han debate .S. scabiei mites isolated from 11 populations of six wild ruminant species in Spain, this study aims to describe the genetic structure of the circulating S. scabiei “strains,” namely (i) the number of S. scabiei strains that can be molecularly identified in wild ruminant populations in Spain, and (ii) the epidemiological relationships between S. scabiei and the wild ruminant communities within the main outbreak areas countrywide.Using S. scabiei following morphological criteria [Skin samples from 121 mangy wild ruminants were collected during regular management plan activities or seasonal culling programs between 2011 and 2019 in 11 areas in Spain  [DNA was extracted from individual mites following the HotSHOT Plus ThermalSHOCK technique . A 10× m 44, 45) , 30. PriThree main population genetics analyses were applied to the 266 mite microsatellite outputs: (i) Bayesian clustering, (ii) genetic distance , and iii) principal component analysis (PCA). The first one requires Hardy–Weinberg equilibrium (HWE), while no assumptions are required for the second and third analyses.Descriptive statistics, including observed and expected heterozygosis , allelic richness (R), and HWE analysis, were carried out in the R 4.0 software environment using the packages Adegenet 2.1.3 and Pegas 0.3 , 32.P values for the HWE test were based on Monte Carlo permutations of alleles. The Bayesian assignment test was computed with STRUCTURE 2.3.4 software [K (for K = 1–20) were run. The ancestry model was selected as the admixture model. The estimation of clusters was performed as previously described [software . Burn-inescribed , using tGenetic distances and multilocus proportion of shared alleles (DPS) among mite populations were computed between all possible pairs of individuals using microsatellite analyzer (MSA 4.0) and Populations 1.2.32 software, and then displayed with interactive Tree of Life (iTOL)  as unrooMultivariate analysis (PCA) was performed with R 4.0 without any preliminary assumptions on the origin of the mite samples. The populations of mites in this analysis were labeled as reported in Table Seventy-three different alleles were detected in the 266 mites isolated from the 11 wild ruminant populations using ten microsatellite loci as molecular markers . The Bayesian assignment test, according to the DK method of Evanno (K = 3) [Significant deviation from HWE was observed overall  , showed The samples within each individual cluster were consistent with an origin-based classification. The genetic distance among all the mites is displayed in the unrooted dendrogram in Fig. Overall, the three different cluster analyses performed in agreement, regardless of HWE, in defining three groups of ruminant-derived mites, consistent with the geographical origin, displayed in Fig. S. scabiei in the mange-affected wild ruminant populations investigated throughout Spain. The three genetic clusters identified revealed that (i) different wild ruminant species were affected by the same S. scabiei strain, and (ii) circulating S. scabiei strains in Spain are both geographically and host-related, although (iii) geographical distance among mange-affected wild ruminant populations is not related to mite strain phylogeny, with distant populations affected by the same S. scabiei strain and close populations hosting different strains.The cluster analyses performed in our study consistently identified three main genetic clusters of C. elaphus and C. pyrenaica, respectively) were also geographically limited to a single region or neighboring areas. Conversely, the third cluster (Cazorla/Asturias-derived) encompassed multi-host systems  and referred to different areas in the Southeast, Northwest and more recently Northeast of the Iberian Peninsula  and the Alpine ibex (Capra ibex) play a reservoir role, whereas the red and roe deer and European mouflon are mere spillover hosts despite their abundance and sympatry with the aforementioned native caprines [ual host , 37. Litmunities –21. In Smunities , 8, 12. caprines .S. scabiei clusters  might imply the existence of a new Sarcoptes-strain that started to spread after the index case was recorded in the local ungulate population of La Rioja  in the main populations of free-ranging wild ruminants in Spain, pointing to a probable origin from livestock in most of the populations affected by sarcoptic mange. Scabies-free populations of wild ungulates in Spain may be exposed to infected domestic caprines in the future. Therefore, further genetic investigations, including livestock, are required to fine-tune the epidemiological role of domestic ungulates in the spread of sarcoptic mange at the wildlife–livestock interface in the Iberian Peninsula. The use of molecular tools such as the microsatellite markers applied to the genetic epidemiology of S. scabiei might have important health implications in wildlife restocking management plans and livestock movements, as recently proved in other wildlife species [S. scabiei into host-related variants (varietates) may be insufficient to represent the complexity that growing molecular epidemiological studies in natural scenarios seem to reveal. We expect that the use of next-generation sequencing such as whole genome sequencing will soon be applied to improve the robustness and repeatability of phylogenetic studies of S. scabiei in animals and humans.This study establishes the current distribution of  species . At the Additional file 1: Table S1. Raw microsatellite alleles of the 10 SARMS microsatellite loci for Sarcoptes scabiei mites. A total of 266 mites were collected from skin samples and skin scrapings of 121 ruminants belonging to six species, namely Iberian ibex (76), Cantabrian chamois (16), red deer (18), roe deer (2), aoudad (1), and European mouflon (1), from 11 sampling locations in Spain.Additional file 2: Table S2. Results of the Hardy–Weinberg equilibrium test at locus (rows) and populations (columns) showing P values from the Monte Carlo test. P values less than 0.05 (*) and 0.01 (**) are considered significant.


Speranskia tuberculata (Euphorbiaceae), to determine its glacial refugia and postglacial demographic history. To this end, we sampled 423 individuals from 38 populations covering its entire geographic distribution. Three chloroplast DNA (cpDNA) fragments, two low-copy nuclear genes, and six nuclear microsatellites (nSSRs) were used and supplemented with ecological niche modeling (ENM) to infer the phylogeographic history of this species. Populations with private haplotypes and high haplotype diversity of cpDNA are mainly located in the CLP or scattered around northeastern China and the coastal region. Spatial expansion, detected using a neutrality test and mismatch distribution, may have resulted in a widely distributed ancestral cpDNA haplotype, especially outside of the CLP. For nuclear DNA, private haplotypes are also distributed mainly in the CLP. In nSSRs, STRUCTURE clustering identified two genetic clusters, which are distributed in the west (western cluster) and east (eastern cluster), respectively. Many populations belonged, with little to no admixture, to the western cluster while (hardly) pure populations of the eastern cluster were barely found. Genetic differentiation is significantly correlated with geographic distance, although genetic diversity is uniformly distributed. ENM suggests that the distribution of S. tuberculata has recently expanded northwards from the southern CLP, whereas it has experienced habitat loss in the south. Thus, S. tuberculata populations probably survived the last glacial maximum (LGM) in the southern CLP and experienced post-glacial expansion. Wind-dispersed pollen could bring the majority of genotypes to the front during spatial expansion, resulting in uniformly distributed genetic diversity. Based on evidence from molecular data and vegetation and climate changes since the LGM, we conclude that drought-enduring species, especially herbaceous species, are likely to have persisted in the CLP during the LGM and to have experienced expansion to other regions in northern China.The significance of the Chinese Loess Plateau (CLP) in maintaining biodiversity for northern China has rarely been shown, as previous phylogeographic studies are mostly woody species and they have revealed that Quaternary refugia are mainly located in mountain regions. We selected a drought-enduring endemic herb,  The Chinese Loess Plateau (CLP), which spans from 34 – 40°N and 101 – 113°E in northern China, contains heterogeneous topography and climate  and is aPinus tabulaeformis, Quercus liaotungensis , while the present coniferous and deciduous forests experienced southward retreat to below 30°N . Phylogeungensis  and a shavidiana , as diffavidiana .P. tabulaeformis  Baillon (Euphorbiaceae), belonging to an East Asian endemic genus with two species only, was selected. This species is a drought-enduring endemic herb in northern China that is mainly distributed in the CLP and adjacent areas, where it usually occurs in dry habitats such as xerothermophilous grasslands, sparse thickets, and forest edges. Its pollen is dispersed by wind, while seeds are dispersed by gravity . Its generation time is about one year base on personal observations. Genetic variation estimated from chloroplast (cp) and low-copy nuclear (n) DNA as well as nuclear microsatellites (nSSRs) was combined with ecological niche modeling (ENM) to investigate (a) the population genetic structure of S. tuberculata and to test (b) whether any refugia were located in the CLP.To assess the significance of the CLP for preserving biodiversity, S. tuberculata individuals representing 38 populations were sampled through its entire geographic distribution  developed using transcriptome data , and nucleotide diversity (π) were calculated in DnaSP. The most parsimonious networks for both plastid and nuclear data were inferred using Network 5.0  from zero was used to test for Hardy-Weinberg equilibrium using FSTAT 2.9.3 , observed heterozygosity (HO), gene diversity (HS), overall gene diversity (HT), and among-population differentiation (FST) were calculated using FSTAT. For all populations, AO, HO, and expected heterozygosity (HE) were calculated in GenAlEx 6.5  and PAR  in populations with more than eight samples were calculated in hp-rare 1.0 using rarefaction with a sample number of eight  were determined by LnP(D), the change in log-likelihood of the data for each run  between successive K-values  climate variables (1) with 2.5 arc-min resolution were used to model the niche at present  indicated significant spatial expansion for all populations.Both mismatch analysis  that is significantly deviated from zero, suggesting that these populations are not under Hardy-Weinberg equilibrium  indicated a significant correlation between genetic differentiation and geographic distance among all sampled populations.Null alleles were not found in the six nSSR loci, and no significant genotypic disequilibrium was observed among the 15 locus pairs in any populations. Several populations had a fixation index  gradually increased from K = 2 to K = 11  indicate good accuracy of model predictions. At present, l region . During l region . Comparian Basin .S. tuberculata was investigated using multiple genetic markers and potential habitat modeling. Chloroplast and nuclear DNA as well as ENM consistently support the hypothesis that S. tuberculata survived the unsuitable climate in the macrorefugium in the southern CLP and in multiple distant microrefugia. In contrast, nSSRs are ambiguous in inferring refugia and postglacial demographic history.In the present study, the phylogeography history of S. tuberculata is located there  that show a genetic mixture in northern China  are derived from the ancestral haplotype (H1), indicating the CLP may be the source of genotypes in southwestern China.The CLP contributes not only to the biodiversity of northern China, but also to other regions in East Asia. First, The present phylogeographic work is an important supplement to previous studies in East Asia, which are much more numerous for northwestern China , subtropThe datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/J-WY and BT conceived the ideas. H-YW, M-JF, and PZ contributed to the sampling and the data analyses. J-WY and BT wrote the manuscript. All authors have read and approved the final manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Mauritia flexuosa. We used a genome scan framework, sampling 16,262 single-nucleotide polymorphisms (SNPs) with target sequence capture in 264 individuals from 22 populations in rainforest and savanna ecosystems. We identified outlier loci as well as signal of adaptation using Bayesian correlations of allele frequency with environmental variables and detected both selective sweeps and genetic hitchhiking events. Functional annotation of SNPs with selection footprints identified loci affecting genes related to adaptation to environmental stress, plant development, and primary metabolic processes. The strong differences in climatic and soil variables between ecosystems matched the high differentiation and low admixture in population Bayesian clustering. Further, we found only small differences in allele frequency distribution in loci putatively under selection among widespread populations from different ecosystems, with fixation of a single allele in most populations. Taken together, our results indicate that adaptive selective sweeps related to environmental stress shaped the spatial pattern of genetic diversity in M. flexuosa, leading to high similarity in allele frequency among populations from different ecosystems.Despite the global importance of tropical ecosystems, few studies have identified how natural selection has shaped their megadiversity. Here, we test for the role of adaptation in the evolutionary success of the widespread, highly abundant Neotropical palm  The geographic distribution of genetic diversity results from the interplay between demographic forces , mutation, recombination, and natural selection . The stuEvidence of local adaptation has been identified in plants from temperate climates , yet onlPinus taeda,  is one of the most hyperdominant species in Amazonia and is common in swampy environments  with target sequence capture approach. Coalescent simulations were used to reconstruct the demographic history of the species based on putatively neutral SNPs in an attempt to disentangle the effects of demography (genetic drift and gene flow) and natural selection on the distribution of genetic diversity. Because of the contrasting environmental conditions of the different ecosystems, i.e., tropical rain forest and seasonal savanna, we expect to find local adaptation and high differentiation in allele frequencies among ecosystems.Here, we test between local adaptation and genetic drift as a driver of the evolutionary success characterizing the high abundance and broad geographic range of the hyperdominant species M. flexuosa throughout its geographic range  and expected heterozygosity using He) and inbreeding coefficient (f) using Arlequin v. 3.5 (FCT) and among populations within ecosystems (FSC). We also analyzed the differentiation among river basins (FCT), among populations within river basins (FSC), and inbreeding coefficient (FIS). Significance levels of 0.05 for each estimate were determined with 10,000 permutations.To characterize population genetic diversity across all SNP loci, we estimated expected heterozygosity under Hardy–Weinberg equilibrium (n v. 3.5 . We usedR2 > 0.30) using the option —indep-pairwise 50 5 0.3. The list of cleaned and LD-pruned SNPs was checked for SNPs with positive selection signal, and none were identified, based on Outflank and Bayenv2 results. Therefore, this list of potentially neutral and high-quality SNPs was used to estimate genetic diversity and to perform an AMOVA. Finally, we used Bayesian clustering implemented in fastSTRUCTURE software  pruned loci. We used PLINK 1.9  to elimisoftware  to identSelector , with a Selector . To geneSelector . For thiM. flexuosa, we modeled the demographic history and performed simulations for 3,500 potentially neutral loci. We simulated two demographic scenarios derived from ecological niche modeling (see t = 0) to t = 525 generations ago  were obtained for the 22 populations sampled. The four bioclimatic variables were identified by low collinearity in factorial analysis with Varimax rotation. These four variables explained 90.4% of the total environmental variation among the 22 populations  was similar to the diversity obtained with only putatively neutral loci .The average SNP density was 1.06 SNP/100 bp  with low admixture in populations from different ecosystems  and negative and significant inbreeding coefficient , showing higher frequency of mating between unrelated individuals than expected at random, as predicted for a dioecious species. Genetic differentiation was higher for the 3,470 putatively neutral loci , and the inbreeding coefficient was significant . Hierarchical AMOVA showed low, but significant differentiation among ecosystems , for the entire dataset  and for the 3,470 putatively neutral, LD-pruned loci . Differentiation among populations within ecosystems was low for the entire dataset  and for the putatively neutral loci . Differentiations among river basins  and among populations within river basins  were low but significant for the entire dataset, as well as for the 3,470 putatively neutral, LD-pruned loci . Genetic differentiation among pairs of populations was significantly correlated to geographical distance , which is an important requirement for protein trafficking in cells and plant growth in thaliana , was sigthaliana . The Mg thaliana , was corthaliana . This coA. thaliana  and the transcriptome size of election . Thus, iCTF = 0.063) and within ecosystems (FSC = 0.064). In addition, the Bayesian clustering showed some admixture among populations, especially from Amazonia and Cerrado. These results contrast with the higher differentiation for microsatellite loci , most likely due to higher mutation rates at microsatellite loci, leading to higher heterozygosity and differentiation. While SNPs are biallelic and evolve under an infinite sites model, microsatellites are multiallelic loci and evolve under stepwise and two-phase mutation models . It is important to note that enotypes . We belienotypes  with a mle calls .M. flexuosa in swampy microhabitats.Using target sequence capture SNP genotyping to generate data for over 16,000 SNPs, we unravel the evolutionary history of a hyperdominant palm species. Our findings suggest that selection together with migration led to the spread of alleles with higher fitness among populations from different ecosystems and promoted the evolutionary success of the widespread, highly abundant Neotropical palm PRJNA588981).Data and additional supporting information may be found in the online version of this article as supporting information. DNA datasets are available in GeneBank database (access number: BioProject ID RC and CB conceived the experiment. RC and CB funded the work. WM conducted the experiment. WM, LV, EN, and RC performed the analysis including assembling, annotation, and curated the data. RC wrote the first draft of the manuscript. All co-authors contributed to the final version of the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.