Bayesian co-estimation of selfing rate and locus-specific mutation rates for a partially selfing population

We present a Bayesian method for characterizing the mating system of populations reproducing through a mixture of self-fertilization and random outcrossing. Our method uses patterns of genetic variation across the genome as a basis for inference about pure hermaphroditism, androdioecy, and gynodioecy. We extend the standard coalescence model to accommodate these mating systems, accounting explicitly for multilocus identity disequilibrium, inbreeding depression, and variation in fertility among mating types. We incorporate the Ewens Sampling Formula (ESF) under the infinite-alleles model of mutation to obtain a novel expression for the likelihood of mating system parameters. Our Markov chain Monte Carlo (MCMC) algorithm assigns locus-specific mutation rates, drawn from a common mutation rate distribution that is itself estimated from the data using a Dirichlet Process Prior (DPP) model. Among the parameters jointly inferred are the population-wide rate of self-fertilization, locus-specific mutation rates, and the number of generations since the most recent outcrossing event for each sampled individual

Pratylenchus smoliki, a new nematode species (Pratylenchidae: Tylenchomorpha) from the Great Plains region of North America

Pratylenchus smoliki is a new species of root-lesion nematode described from corn-soybean production fields in the Central Great Plains of North America. It is characterized by populations with relatively abundant males, two lip annuli, females with a round functional spermatheca and a conoid to subcylindrical tail with a non-crenate, smooth terminus. In host preference tests, corn and wheat produce the largest nematode populations, whereas sorghum and soybeans produce less than 20% the numbers observed on corn. Scanning electron microscopy reveals that the en face patterns compare to those seen in Pratylenchus pseudocoffeae, P. scribneri, P. hexincisus, and P. alleni. The pattern is described as rectangular to trapezoidal subdorsal and subventral lips adjoining oral disc, but with a clear demarcation between the oral disc and the subdorsal and subventral sectors. A Maximum Likelihood COI tree recognizesP. smoliki as a moderately-well-supported clade with several haplotype subgroups. A Maximum Likelihood partial 28S tree provides strong support for the P. smoliki clade and reinforces the close relationships between species with similar en facepatterns. Topotype specimens of P. alleni were demonstrably different from P. smoliki using DNA markers. The geographic range of P. smoliki overlaps with the ranges of P. alleni, P. scribneri, P. neglectus, P. hexicisus, and P. dakotaensis. The observed host range (corn, rye, sunflower, and wheat) suggests that P. smoliki may be native to the tallgrass prairie region of the Great Plains

A Bayesian Approach to Inferring Rates of Selfing and Locus-Specific Mutation.

We present a Bayesian method for characterizing the mating system of populations reproducing through a mixture of self-fertilization and random outcrossing. Our method uses patterns of genetic variation across the genome as a basis for inference about reproduction under pure hermaphroditism, gynodioecy, and a model developed to describe the self-fertilizing killifish Kryptolebias marmoratus. We extend the standard coalescence model to accommodate these mating systems, accounting explicitly for multilocus identity disequilibrium, inbreeding depression, and variation in fertility among mating types. We incorporate the Ewens sampling formula (ESF) under the infinite-alleles model of mutation to obtain a novel expression for the likelihood of mating system parameters. Our Markov chain Monte Carlo (MCMC) algorithm assigns locus-specific mutation rates, drawn from a common mutation rate distribution that is itself estimated from the data using a Dirichlet process prior model. Our sampler is designed to accommodate additional information, including observations pertaining to the sex ratio, the intensity of inbreeding depression, and other aspects of reproduction. It can provide joint posterior distributions for the population-wide proportion of uniparental individuals, locus-specific mutation rates, and the number of generations since the most recent outcrossing event for each sampled individual. Further, estimation of all basic parameters of a given model permits estimation of functions of those parameters, including the proportion of the gene pool contributed by each sex and relative effective numbers

Quantifying ice cliff evolution with multi-temporal point clouds on the debris-covered Khumbu Glacier, Nepal

Measurements of glacier ice cliff evolution are sparse, but where they do exist, they indicate that such areas of exposed ice contribute a disproportionate amount of melt to the glacier ablation budget. We used Structure from Motion photogrammetry with Multi-View Stereo to derive 3-D point clouds for nine ice cliffs on Khumbu Glacier, Nepal (in November 2015, May 2016 and October 2016). By differencing these clouds, we could quantify the magnitude, seasonality and spatial variability of ice cliff retreat. Mean retreat rates of 0.30–1.49 cm d−1 were observed during the winter interval (November 2015–May 2016) and 0.74–5.18 cm d−1 were observed during the summer (May 2016–October 2016). Four ice cliffs, which all featured supraglacial ponds, persisted over the full study period. In contrast, ice cliffs without a pond or with a steep back-slope degraded over the same period. The rate of thermo-erosional undercutting was over double that of subaerial retreat. Overall, 3-D topographic differencing allowed an improved process-based understanding of cliff evolution and cliff-pond coupling, which will become increasingly important for monitoring and modelling the evolution of thinning debris-covered glaciers

Horizontal, Anomalous U(1) Symmetry for the More Minimal Supersymmetric Standard Model

We construct explicit examples with a horizontal, ``anomalous'' $U(1)$ gauge group, which, in a supersymmetric extension of the standard model, reproduce qualitative features of the fermion spectrum and CKM matrix, and suppress FCNC and proton decay rates without the imposition of global symmetries. We review the motivation for such ``more'' minimal supersymmetric standard models and their predictions for the sparticle spectrum. There is a mass hierarchy in the scalar sector which is the inverse of the fermion mass hierarchy. We show in detail why DeltaS = 2 FCNC are suppressed when compared with naive estimates for nondegenerate squarks.Comment: Revised version clarifies calculation of FCNC amplitudes and rules out one model considered previousl

Schiedea haakoaensis, a new facultatively autogamous species of Schiedea sect. Mononeura (Caryophyllaceae) from the Hawaiian Islands

In 2016 during a survey for potential fencing of the Ha‘akoa unit on windward Mauna Kea, Hawai‘i Island (Hawaiian Islands) a single plant of the genus Schiedea was discovered. No species of the genus had ever been known to occur in this area, and only three species of Schiedea were known previously from Hawai‘i Island. Two are vining species and the third is a coastal subshrub. The single plant obviously represented an interesting find, and because the plant was vegetative another visit was scheduled to collect a flowering specimen, but by then the plant had died. Soil taken from the site with seeds in the soil produced two plants, one of which flowered in cultivation in 2021. A study of this individual indicated it was a member of Schiedea sect. Mononeura, characterized by erect to ascending habit, quadrangular stems, seeds not persistent on the placenta and readily dispersing from the dehisced capsule, and flowers facultatively autogamous. With the discovery of this new species there are 35 species in this Hawaiian endemic genus

Conservation of oceanic island floras: Present and future global challenges

Currentthreatstotheplanet’sbiodiversityareunprecedented,andtheyparticularlyimperilinsular floras.Inthisinvestigation,weusethethreatfactorsidentifiedbytheMillenniumEcosystem Assessmentasthemaindriversofbiodiversitylossonislandstodefineandrank13current,continuing threatstotheplantdiversityofninefocalarchipelagoswherevolcanicorigin(orintheSeychellesa prolongedisolationafteracontinentalorigin)hasproducedahighdegreeofendemicityandfragilityin the faceofhabitatalteration.Wealsoconductaglobalendangermentassessmentbasedonthe numbersofinsularendemicplantsintheendangered(EN)andcriticallyendangered(CR)IUCN categoriesfor53islandgroupswithanestimated9951endemicplantspecies,providinga representativesampleoftheworld’sinsularsystemsandtheirfloristicrichness.Ouranalysesindicate that isolationdoesnotsignificantlyinfluenceendangerment,butplantendemicsfromverysmall islandsaremoreoftencriticallyendangered.Weestimatethatbetween3500and6800oftheestimated 70,000 insularendemicplantspeciesworldwidemightbehighlythreatened(CR+EN)andbetweenca. 2000 and2800ofthemincriticaldangerofextinction(CR).Basedontheseanalyses,andona worldwideliteraturereviewofthebiologicalthreatfactorsconsidered,weidentifychallenging questionsforconservationresearch,asking(i)whatarethemosturgentprioritiesfortheconservation of insularspeciesandfloras,and(ii)withtheknowledgeandassetsavailable,howcanweimprovethe impactofconservationscienceandpracticeonthepreservationofislandbiodiversity?Ouranalysis indicatesthatthesynergisticactionofmanythreatfactorscaninducemajorecologicaldisturbances, leadingtomultipleextinctions.Wereviewweaknessesandstrengthsinconservationresearchand managementintheninefocalarchipelagos,andhighlighttheurgentneedforconservationscientiststo shareknowledgeandexpertise,identifyanddiscusscommonchallenges,andformulatemulti- disciplinaryconservationobjectivesforinsularplantendemicsworldwide.Toourknowledge,thisisthe mostup-to-dateandcomprehensivesurveyyettoreviewthethreatfactorstonativeplantsonoceanic islandsanddefinepriorityresearchquestions

Supraglacial ponds regulate runoff from Himalayan debris-covered glaciers

Meltwater and runoff from glaciers in High Mountain Asia is a vital freshwater resource for one fifth of the Earth's population. Between 13% and 36% of the region's glacierized areas exhibit surface debris cover and associated supraglacial ponds whose hydrological buffering roles remain unconstrained. We present a high-resolution meltwater hydrograph from the extensively debris-covered Khumbu Glacier, Nepal, spanning a seven-month period in 2014. Supraglacial ponds and accompanying debris cover modulate proglacial discharge by acting as transient and evolving reservoirs. Diurnally, the supraglacial pond system may store >23% of observed mean daily discharge, with mean recession constants ranging from 31 to 108 hours. Given projections of increased debris-cover and supraglacial pond extent across High Mountain Asia, we conclude that runoff regimes may become progressively buffered by the presence of supraglacial reservoirs. Incorporation of these processes is critical to improve predictions of the region's freshwater resource availability and cascading environmental effects downstream

Asymmetrical Gene Flow in a Hybrid Zone of Hawaiian Schiedea (Caryophyllaceae) Species with Contrasting Mating Systems

Asymmetrical gene flow, which has frequently been documented in naturally occurring hybrid zones, can result from various genetic and demographic factors. Understanding these factors is important for determining the ecological conditions that permitted hybridization and the evolutionary potential inherent in hybrids. Here, we characterized morphological, nuclear, and chloroplast variation in a putative hybrid zone between Schiedea menziesii and S. salicaria, endemic Hawaiian species with contrasting breeding systems. Schiedea menziesii is hermaphroditic with moderate selfing; S. salicaria is gynodioecious and wind-pollinated, with partially selfing hermaphrodites and largely outcrossed females. We tested three hypotheses: 1) putative hybrids were derived from natural crosses between S. menziesii and S. salicaria, 2) gene flow via pollen is unidirectional from S. salicaria to S. menziesii and 3) in the hybrid zone, traits associated with wind pollination would be favored as a result of pollen-swamping by S. salicaria. Schiedea menziesii and S. salicaria have distinct morphologies and chloroplast genomes but are less differentiated at the nuclear loci. Hybrids are most similar to S. menziesii at chloroplast loci, exhibit nuclear allele frequencies in common with both parental species, and resemble S. salicaria in pollen production and pollen size, traits important to wind pollination. Additionally, unlike S. menziesii, the hybrid zone contains many females, suggesting that the nuclear gene responsible for male sterility in S. salicaria has been transferred to hybrid plants. Continued selection of nuclear genes in the hybrid zone may result in a population that resembles S. salicaria, but retains chloroplast lineage(s) of S. menziesii