Jointly Modeling Species Niche and Phylogenetic Model in a Bayesian Hierarchical Framework

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Июль 8, 2022

ABSTRACT When studying how species will respond to climatic change, a common goal is predict distributions change through time. Environmental niche models (ENMs) are commonly used estimate species’ environmental from observed patterns of occurrence and predictors. However, often shaped by non-environmental factors–including biotic interactions dispersal barriers—truncating estimates. Though truncated may accurately present-day distribution within the sampled area, this accuracy decreases when predicting at different places under conditions. Modeling in phylogenetic framework leverages clade’s shared evolutionary history pull estimates closer towards conserved values farther away specific biases. We propose new Bayesian model estimation implemented R called BePhyNE (Bayesian Phylogenetic Niche Estimation). Under our model, ENM parameters transformed into biologically interpretable continuous optimum, breadth, tolerance evolving as multivariate Brownian motion. Through simulation analyses, we demonstrate precision that improve phylogeny size increases. also on eastern United States Plethodontid salamanders recover accurate niche, even data lacking entirely informed model. Our demonstrates novel where changes can be studied forwards backwards time understand ancestral ranges, specialization, niches data-deficient species.

Язык: Английский

---

Mitochondrial composition of and diffusion limiting factors of three social wasp genera Polistes, Ropalidia, and parapolybia (Hymenoptera: Vespidae)

BMC Ecology and Evolution, Год журнала: 2022, Номер 22(1)

Опубликована: Май 12, 2022

Abstract Background Social wasps Polistes , Ropalidia and Parapolybia belonging to the subfamily Polistinae, have obviously different distribution patterns, yet factors leading this difference remain unknown. Results The 17 newly sequenced mitogenomes of contain 37 genes, there are obvious differences among compositions three genera. monophyly genus a monophyletic Ropalidiini: ( + ) concordant with previous morphological analysis Polistinae. Our inferred divergence time demonstrates (at around 69 Ma) was diverged earlier than 61 Ma). rearrangement both trnY trnL1 shared by all In addition, unique TDRL derived at Ma is detected in contains Reversal which may derive Ma. Hereafter, possibility elaborated that originated Aisa then dispersed from Africa South America, spread Southeast Asia Australia. At last, continental drift Quaternary Ice Ages be two main limiting current distributions Conclusions Obvious occur mitochondrial composition . According reconstructed time-calibrated framework, it inquired drifts climate mainly diffusion

Язык: Английский

---

A New Paralog Removal Pipeline Resolves Conflict between RAD-seq and Enrichment

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2020, Номер unknown

Опубликована: Окт. 27, 2020

ABSTRACT Target enrichment and RAD-seq are well-established high throughput sequencing technologies that have been increasingly used for phylogenomic studies, the choice between methods is a practical issue plant systematists studying evolutionary histories of biodiversity relatively recent origins. However, few studies compared congruence conflict results from two within same group organisms, especially in plants, where extensive genome duplication events may complicate analyses. Unfortunately, currently widely pipelines target data analysis do not vigorous procedure remove paralogs Hyb-Seq data. In this study, we employed Angiosperm 353 genes biogeographic Hamamelis (the witch-hazels) Castanea (chestnuts), classic examples exhibiting well-known eastern Asian-eastern North American disjunct distribution. We these side by developed new pipeline (PPD) with more removal putative The considers both sequence similarity heterozygous sites at each locus identification paralogous. our to construct robust datasets comparison downstream analyses on genera. Our demonstrated PPD identified many than popular method HybPiper. Comparisons tree topologies divergence times showed significant differences HybPiper pipeline, likely due error signals paralogous undetected HybPiper, but trimmed PPD. found phylogenies estimated Hyb-Seq-PPD were largely congruent. highlight importance data, discuss merits Hyb-Seq. Finally, phylogenetic resulted well-resolved species relationships, revealed ancient introgression Biogeographic including fossil complicated history genus involving multiple intercontinental dispersals local extinctions areas outside taxa’s modern ranges Paleogene Neogene. study demonstrates value additional steps filtering gene content such as described study. [RAD-seq, Hyb-Seq, paralogs, , Asia-eastern America disjunction, biogeography, introgression]

Язык: Английский

---

In memory of Professor Tang Yan‐Cheng: New perspectives in systematic and evolutionary biology

Journal of Systematics and Evolution, Год журнала: 2020, Номер 58(5), С. 527 - 532

Опубликована: Авг. 22, 2020

In China, three institutes for botanical research were established in the 1920s, namely Department of Botany, Biological Laboratory Science Society China (1922, Nanjing), Fan Memorial Institute Biology (1928, Peiping), and Peiping Academy Sciences (1929, Peiping). Since then, plant taxonomy, systematics, phytogeography have advanced prospered as scientific disciplines China. Among great botanists who studied at those institutes, others that over following 100 years, was Prof. Tang (surname) Yan-Cheng (given name) (汤彦承, abbreviated Y. C. Tang) (7 July 1926–6 August 2016). Professor a well-known highly respected taxonomist an influential professor Chinese Sciences, Beijing. played pivotal role leading taxonomic/systematic from 1970s into 1990s. He not only provided new insights flora, but also helped to develop botany according what then cladistic methods train generations botanists. During his career, keenly promoted novel theories taxonomic systematic methods, he encouraged application up-to-date experimental approaches analytical methodologies study plants. His had global implications large, widely distributed families better understanding origin evolution East Asian flora (see Wang et al., 2020a more details below). Therefore, this special issue, we compiled articles reflect current advances honor contributions Tang. The herein, including reviews original articles, represent perspectives systematics evolution, present integrates multifaceted data interdisciplinary approaches. Several concern taxa depth by or focus interest. Modern biology originated 1960s with developed expounded Hennig (Hennig, 1966; Funk, 2018). past 30 discipline has been transformed use molecular phylogenetics (Hillis 1996; Soltis 1998). Subsequent advancements technology, phylogenetic methodologies, comparative led explosion phylogeny-based studies. results relationships organisms which share our planet (Chase 1993; San Mauro & Agorreta, 2010; Losos 2013; Hinchliff 2015; Soltis, 2016; 2018; Bakker 2020). Moreover, recent efforts reconstructing tree life, integrating sharing across disciplines, digitizing biological collections, harvesting big high-throughput DNA sequencing, development genetic tools (Wen 2015, 2017; Leebens-Mack 2019; 2020) empowered evolutionary undertake integrative studies previously impossible (e.g., Chanderbali Ma 2017a, 2017b; Ellwood Hodel Landis Lewin Lu Dong 2019). Plant plays elucidating assembly Earth's flora. central applications is sustenance, use, conservation resources, especially under many threats Anthropocene, modern threat climate change. How will species adapt environmental changes are constraints drivers adaptation? These questions ecology biology. Changing climates warming require urgent address these through characterizing various factors affecting rate capacity adaptability Genetic variability, population structure, genes/traits selected local adaptation biotic abiotic changes/stresses lay foundation its survival. Our knowledge such traits regard forest trees crop particularly important predicting sustainability forests crops changing environments ecological adaptation. At present, simultaneously broad scope detailed levels genes feasible. By interfacing cutting-edge tools, can gain comprehensive advance regarding climate. Anderson Song (2020) overview progress, gaps, perspectives, well plants They evaluate impact change on selection, adaptation, interactions. discuss effects gene flow phenotypic plasticity way respond argue eco-evolutionary dynamics facilitate plant's adaptive potential rapid intense Additionally, they review most using omics biotechnologies dissect basis conclude key gaps exist, expanding foci model diverse array non-model natural systems, identifying candidate validating their functions, discovery causal fitness tests conditions, single stress multiple complex interactive nature environments. highlight importance employing cross-disciplinary integrate ecology, genetics, systems accurately predict probability persist environment. bridges between subdisciplines inspires innovative work field expanded diversity level genomic variation structure fine scales, identify loci associated along spatial gradients climate, soil, disease). For example, Pais colleagues made species, Cornus florida L., landscape phylogeography, genomics, metabolomics, genome-wide association (GWAS) traditional community (Pais 2017, 2018, al. (2017) used approach Genotyping Sequencing (GBS) than 50 selection (differing temperature, precipitation, soil nutrients southern Appalachian Mountains, Piedmont Plateau, coastal plain North Carolina). L. (colloquially, “flowering dogwood”), some determined be dogwood anthracnose disease, seriously threatened populations. non-targeted liquid chromatography–mass spectrometry (LC-MS) profiling GWAS, (2018) discovered production certain groups metabolites. One locus represents L-type lectin domain containing receptor kinase known providing immunity disease (Singh Zimmerli, 2013). report findings cover whole range noted above again identified one selection. This particular locus, whose function may validated genome editing, provides strong future related resistance. Some putatively exhibited abrupt turnover allele frequencies populations borders Hot Continental ecoregion anthracnose. Trees harboring alleles vary among ecoregions breeding programs goal developing hardy cultivars florida, popular ornamental species. study, evaluated patterns compared found distribution further explored relationship fungal sequences contained GBS sampled visual records locations, informative detecting disease. Understanding diversification remains challenge (Losos New insights, however, increasingly being derived incorporate phylogenomics, biogeography, modeling, analyses elucidate spatiotemporal climatic niche divergence speciation processes morphological adaptations Blaine Marchant Visger Yu Hearn Fu Gao Kawahara Martín-Bravo Du Two papers issue (Lindelof 2020; Zhou shed light history eastern Asian–eastern American (EA–ENA) pattern geographic disjunction post-isolation disjunct lineages. EA–ENA biogeographic attracted attention phylogenomic era Li Zhang conducted vigorous generated microfluid PCR Fluidigm sequencing. different dating assessed conflict trees, fossil calibrations. included constructing comprehensively dated phylogeny Fossilized Birth Death analysis. applied user-defined time slice inter-areal dispersal probabilities divergence–extinction–cladogenesis (DEC) method capture historical barriers migration. examining niches, sought understand likely shaped sister clades disjunctions. contains Lindelof (2020), based RAD-seq data, lineage (Cornaceae) bears blue, white, black fruits. authors via analyses. On above, reconstructed examined EA ENA pairs. evidence rates shifts tested hypothesis morphostasis pairs greater (Qian Ricklefs, 2000; Xiang 2004; Lee Gaynor roles biogeography shaping Diapensiaceae combing nuclear plastid enrichment newly Angiosperm 353 probes. demonstrated utility flanking regions resolving within families. Abundant publicly available databases increased sequencing capacity, coupled availability enabled considerable phylogenetics. field, integration distributional employed biodiversity, biodiversity hot spots refugia conservation, uncover contemporary communities Mishler 2014; Chen 2016, Pollock Miller Ye Spatial powerful regional scales life. Hu updating life vascular level, genus-level previous framework (Chen updated phylogeny, listed non-monophyletic genera investigation. both genus regional-scale serve other intersection functional ecology. fundamental goals transform gained reconstructions predictive stable classification system, reflecting histories public Le Increasingly, robust phylogenies extensive complete sampling classification. (2020b) revised Magnolia Magnoliaceae, skimming taxon sampling. Similarly, chloroplast Diapensia status several Su collection-based clarify boundaries Stachyuraceae, family endemic Asia. Collection-based allow without expense visiting geographically disparate sites. Such enable simultaneous morphologically distinguishing characteristics resolved (Willis 2017). All (Hu clarified debates propose treatments large amount data. Furthermore, Magnolia, particular, prove useful horticulturally genus. all elucidated space transforming lies definition delineation. Although concepts proposed, delineating major taxonomy active topic systematics. Hong proposes explicit statistics-based gen-morph concept bridge properties offer easily operable work. outcrossing Paeonia argues delimitation accomplished statistical discontinuity two independent traits. verifies discontinuities features good proxy distinction morphology-based classifications, A Brief Biography Late citations) born Xiaoshan, Zhejiang Province, graduated Tsinghua [Qinghua] University 1950 joined Taxonomy (now Botany) Sciences. From October 1958 1960, scholar Komarov Botanical Research Moscow, former Soviet Union. 1972 1981, director Biogeography Botany. As organizers state projects Iconographia Cormophytorum Sinicorum (Illustrated Vascular Plants China) Flora Reipublicae Popularis Sinicae (FRPS), wrote edited volumes series books. received National Natural First Prize (one winners, Wentsi) Third latter. Through own professional activities, actively advancement prosperity versatile knowledgeable scholar, excellent mentor friend community. excelled classic literature, nomenclature Latin, concepts, cladistics. paid close latest international developments taxonomy/systematics introduced ideas, theories, timely manner. Those endeavors significant broad, base education. 1942 1945, attended Suzhou Taowu Middle School, private institution Shanghai. Due influence teacher, Bingliu, school, advocated ideals “Seven Wise Men Bamboo Forest (竹林七贤),” group scholars, writers, artisans third-century CE followed Taoism, essentially living harmony nature. later enjoyed Zhuangzi (庄子), collection writings fifth third century BCE Taoism. entered College Agriculture St. John's Shanghai, university, undergraduate study. Later, transferred Advanced Class Shanghai Temporary University. 1946, recommended admitted University, China's top universities. Of students time, chose botany. student botany, Wu Zhengyi (Wu Cheng-yih) (1916–2014) morphology Jingyue (1895–1975). teachings Jingyue, complementary, interactive, guiding, inspired instilled him exceptional self-learning habit thinking outside absorbing ideas disciplines. teacher–student friendship Chengyi during Tang's four years half collaboration famous taxonomists. admired remark historian Mr. Wenlan (1893–1969): "板凳要坐十年冷, 文章不写半句空 (Literally: bench sit cold ten no wasteful words written article)". real meaning concentrate pursuit truth before putting pen paper. Notably, did publish peers, novel, thoughtful, influential, regarded. spend dwelling out date (Wang 2020a). continued undiminished rigor until last breath. knowledgeable, modest, easy-going, selflessly dedicated throughout humble honorable person worked tirelessly quietly enhance never honors himself, instead always tried help promote others. research, moral character, continue inspire us privileged know him, well. biography (2020a) where specific discussed. We thank AJ Harris Jun Wen reviewing constructive editing comments article. JX Wang, HN Qin, AM contributing information JSE journal manager Y Liang chief editors J S Ge support.

Язык: Английский

---

Mitochondrial composition of and diffusion limiting factors of three social wasp genera Polistes, Ropalidia, and Parapolybia (Hymenoptera: Vespidae)

Research Square (Research Square), Год журнала: 2021, Номер unknown

Опубликована: Фев. 12, 2021

Abstract Background Social wasps Polistes , Ropalidia and Parapolybia belonging to the subfamily Polistinae, have obviously different distribution patterns, yet factors leading this difference remain unknown. Results In study, mitochondrial genomes (mitogenomes) of 21 species these three wasp genera were used phylogenetic analyses, including 17 newly sequenced ones. It is revealed that both evolutionary selection pressure protein-coding genes (PCGs) gene rearrangement events are related corresponding patterns. addition, our fossil-calibrated divergence time estimation suggests diversification was in Late Cretaceous (~ 69 million years ago, Ma), occurred Tertiary 61 Ma). view history continental drifts, we speculate may spread from Africa South America via Atlantic Ocean rather than Asia America. On other hand, combining climate changes past present-day, it inferred Quaternary Ice Ages temperature could be limitation their present Conclusions There obvious differences composition with ranges. According reconstructed time-calibrated framework, found drifts diffusion limiting genera.

Язык: Английский

---