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Journal articles on the topic 'Ancestral range reconstruction'

Author: Grafiati

Published: 4 June 2021

Last updated: 5 February 2022

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1

Wang, Ning, Rebecca T. Kimball, Edward L. Braun, Bin Liang, and Zhengwang Zhang. "Ancestral range reconstruction of Galliformes: the effects of topology and taxon sampling." Journal of Biogeography 44, no. 1 (2016): 122–35. http://dx.doi.org/10.1111/jbi.12782.

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Guillory, Wilson X., and Jason L. Brown. "A New Method for Integrating Ecological Niche Modeling with Phylogenetics to Estimate Ancestral Distributions." Systematic Biology 70, no. 5 (2021): 1033–45. http://dx.doi.org/10.1093/sysbio/syab016.

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Abstract Ancestral range estimation and projection of niche models into the past have both become common in evolutionary studies where the ancient distributions of organisms are in question. However, these methods are hampered by complementary hurdles: discrete characterization of areas in ancestral range estimation can be overly coarse, especially at shallow timescales, and niche model projection neglects evolution. Phylogenetic niche modeling accounts for both of these issues by incorporating knowledge of evolutionary relationships into a characterization of environmental tolerances. We pres

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Aadland, Kelsey, and Bryan Kolaczkowski. "Alignment-Integrated Reconstruction of Ancestral Sequences Improves Accuracy." Genome Biology and Evolution 12, no. 9 (2020): 1549–65. http://dx.doi.org/10.1093/gbe/evaa164.

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Abstract Ancestral sequence reconstruction (ASR) uses an alignment of extant protein sequences, a phylogeny describing the history of the protein family and a model of the molecular-evolutionary process to infer the sequences of ancient proteins, allowing researchers to directly investigate the impact of sequence evolution on protein structure and function. Like all statistical inferences, ASR can be sensitive to violations of its underlying assumptions. Previous studies have shown that, whereas phylogenetic uncertainty has only a very weak impact on ASR accuracy, uncertainty in the protein se

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Clark, John R., Richard H. Ree, Michael E. Alfaro, Matthew G. King, Warren L. Wagner, and Eric H. Roalson. "A Comparative Study in Ancestral Range Reconstruction Methods: Retracing the Uncertain Histories of Insular Lineages." Systematic Biology 57, no. 5 (2008): 693–707. http://dx.doi.org/10.1080/10635150802426473.

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Sýkora, Vit, David García-Vázquez, David Sánchez-Fernández, and Ignacio Ribera. "Range expansion and ancestral niche reconstruction in the Mediterranean diving beetle genus Meladema (Coleoptera, Dytiscidae)." Zoologica Scripta 46, no. 4 (2017): 445–58. http://dx.doi.org/10.1111/zsc.12229.

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Clark, John R., Warren L. Wagner, and Eric H. Roalson. "Patterns of diversification and ancestral range reconstruction in the southeast Asian–Pacific angiosperm lineage Cyrtandra (Gesneriaceae)." Molecular Phylogenetics and Evolution 53, no. 3 (2009): 982–94. http://dx.doi.org/10.1016/j.ympev.2009.09.002.

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Sharma, Prashant P., and Gonzalo Giribet. "The evolutionary and biogeographic history of the armoured harvestmen – Laniatores phylogeny based on ten molecular markers, with the description of two new families of Opiliones (Arachnida)." Invertebrate Systematics 25, no. 2 (2011): 106. http://dx.doi.org/10.1071/is11002.

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We investigated the internal phylogeny of Laniatores, the most diverse suborder of Opiliones, using sequence data from 10 molecular loci: 12S rRNA, 16S rRNA, 18S rRNA, 28S rRNA, cytochrome c oxidase subunit I (COI), cytochrome b, elongation factor-1α, histones H3 and H4, and U2 snRNA. Exemplars of all previously described families of Laniatores were included, in addition to two families – Petrobunidae, fam. nov. and Tithaeidae, fam. nov. – that we erect herein. Data analyses were based on maximum likelihood and Bayesian approaches on static alignments, and included phylogenetic tree estimation

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Kolanowska, Marta, Katarzyna Mystkowska, Marta Kras, Magdalena Dudek, and Kamil Konowalik. "Evolution of the climatic tolerance and postglacial range changes of the most primitive orchids (Apostasioideae) within Sundaland, Wallacea and Sahul." PeerJ 4 (August 31, 2016): e2384. http://dx.doi.org/10.7717/peerj.2384.

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The location of possible glacial refugia of six Apostasioideae representatives is estimated based on ecological niche modeling analysis. The distribution of their suitable niches during the last glacial maximum (LGM) is compared with their current potential and documented geographical ranges. The climatic factors limiting the studied species occurrences are evaluated and the niche overlap between the studied orchids is assessed and discussed. The predicted niche occupancy profiles and reconstruction of ancestral climatic tolerances suggest high level of phylogenetic niche conservatism within A

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Schmidt-Lebuhn, Alexander N., and Kiarrah J. Smith. "From the desert it came: evolution of the Australian paper daisy genus Leucochrysum (Asteraceae, Gnaphalieae)." Australian Systematic Botany 29, no. 3 (2016): 176. http://dx.doi.org/10.1071/sb16012.

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Present patterns of diversity in the Australian flora have been shaped by increasing seasonality since the Eocene, and by pronounced aridification in the past 3 million years. Arid-zone plants are commonly hypothesised to be the products of radiations of ancestrally temperate or coastal lineages, as in the case of the everlasting paper daisy tribe Gnaphalieae (Asteraceae). However, these inferences are often based on higher-level phylogenies, whereas evolutionary processes in the Australian Gnaphalieae have rarely been studied at the species level. Here, we reconstructed the phylogeny and biog

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Nagy, Jenő, and Jácint Tökölyi. "Phylogeny, Historical Biogeography and the Evolution of Migration in Accipitrid Birds of Prey (Aves: Accipitriformes)." Ornis Hungarica 22, no. 1 (2014): 15–35. http://dx.doi.org/10.2478/orhu-2014-0008.

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Abstract Migration plays a fundamental part in the life of most temperate bird species. The regular, large-scale seasonal movements that characterize temperate migration systems appear to have originated in parallel with the postglacial northern expansion of tropical species. Migratoriness is also influenced by a number of ecological factors, such as the ability to survive harsh winters. Hence, understanding the origins and evolution of migration requires integration of the biogeographic history and ecology of birds in a phylogenetic context. We used molecular dating and ancestral state recons

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Iwanycki Ahlstrand, N., B. Verstraete, G. Hassemer, et al. "Ancestral range reconstruction of remote oceanic island species of Plantago (Plantaginaceae) reveals differing scales and modes of dispersal." Journal of Biogeography 46, no. 4 (2019): 706–22. http://dx.doi.org/10.1111/jbi.13525.

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Gumulya, Yosephine, and Elizabeth M. J. Gillam. "Exploring the past and the future of protein evolution with ancestral sequence reconstruction: the ‘retro’ approach to protein engineering." Biochemical Journal 474, no. 1 (2016): 1–19. http://dx.doi.org/10.1042/bcj20160507.

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A central goal in molecular evolution is to understand the ways in which genes and proteins evolve in response to changing environments. In the absence of intact DNA from fossils, ancestral sequence reconstruction (ASR) can be used to infer the evolutionary precursors of extant proteins. To date, ancestral proteins belonging to eubacteria, archaea, yeast and vertebrates have been inferred that have been hypothesized to date from between several million to over 3 billion years ago. ASR has yielded insights into the early history of life on Earth and the evolution of proteins and macromolecular

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Smith, Martin R. "An Ordovician nectocaridid hints at an endocochleate origin of Cephalopoda." Journal of Paleontology 94, no. 1 (2019): 64–69. http://dx.doi.org/10.1017/jpa.2019.57.

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AbstractNectocaridids are soft-bodied Cambrian organisms that have been controversially interpreted as primitive cephalopods, at odds with the long-held belief that these mollusks evolved from a shell-bearing ancestor. Here, I document a new nectocaridid from the Whetstone Gulf Formation, extending the group's range into the Late Ordovician. Nectocotis rusmithi n. gen. n. sp. possesses a robust internal element that resembles a non-mineralized phragmocone or gladius. Nectocaridids can be accommodated in the cephalopod total group if the earliest cephalopods (1) inherited a non-mineralized shel

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GRISMER, L. LEE, and HAYDEN R. DAVIS. "Phylogeny and biogeography of Bent-toed Geckos (Cyrtodactylus Gray) of the Sundaic swamp clade." Zootaxa 4472, no. 2 (2018): 365. http://dx.doi.org/10.11646/zootaxa.4472.2.9.

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The Sundaic swamp clade of the genus Cyrtodactylus contains nine species that collectively range through Peninsular Malaysia and its associated land bridge islands, Singapore, Sumatra, Java, and Pulau Natuna Besar. Ancestral range reconstruction analyses using BioGeoBEARS based on an updated molecular phylogeny of the nine Sundaic swamp clade species of Cyrtodactylus demonstrated that this lineage evolved in Peninsular Malaysia, dispersed independently to Sumatra and Pulau Natuna Besar, Indonesia and most likely back into Peninsular Malaysia from Sumatra. This scenario is consistent with clima

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Leopardi-Verde, Carlos Luis, and Guadalupe Jeanett Escobedo-Sarti. "Indagando aspectos evolutivos con filogenias: reloj molecular y otras técnicas útiles en biología comparada." Tequio 4, no. 11 (2021): 53–68. http://dx.doi.org/10.53331/teq.v4i11.3158.

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The first step for evolutionary studies is usually to establish a hypothesis of relationships between members of the study group. After this, there is a wide range of possibilities depending on the researcher's interest. This contribution presents the generalities of some of the methodologies most commonly used in macroevolutionary studies: the molecular clock and the reconstruction of ancestral characters. Information on other useful techniques for comparative studies that use a phylogenetic framework is also presented, such as phylogenetic signal estimation, independent contrasts, orthonorma

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Bainard, Jillian D., and Juan Carlos Villarreal. "Genome size increases in recently diverged hornwort clades." Genome 56, no. 8 (2013): 431–35. http://dx.doi.org/10.1139/gen-2013-0041.

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As our knowledge of plant genome size estimates continues to grow, one group has continually been neglected: the hornworts. Hornworts (Anthocerotophyta) have been traditionally grouped with liverworts and mosses because they share a haploid dominant life cycle; however, recent molecular studies place hornworts as the sister lineage to extant tracheophytes. Given the scarcity of information regarding the DNA content of hornworts, our objective was to estimate the 1C-value for a range of hornwort species within a phylogenetic context. Using flow cytometry, we estimated genome size for 36 samples

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Thapa, Ramhari, Randall J. Bayer, and Jennifer R. Mandel. "Phylogenomics Resolves the Relationships within Antennaria (Asteraceae, Gnaphalieae) and Yields New Insights into its Morphological Character Evolution and Biogeography." Systematic Botany 45, no. 2 (2020): 387–402. http://dx.doi.org/10.1600/036364420x15862837791221.

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There is an erratum for this article at: https://doi.org/10.1600/036364420X15959578652451 Abstract—Antennaria are dioecious perennial herbs distributed mainly in the Holarctic Region, with their major center of diversity in the Rocky Mountains of Western North America. The genus comprises 33 known sexual diploid/tetraploid species and at least five polyploid agamic complexes which mostly reproduce by forming asexual seeds. We performed a phylogenetic reconstruction of the 31 sexually-reproducing Antennaria species using a novel target enrichment method that employs custom capture probes design

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Vila, Roger, Charles D. Bell, Richard Macniven, et al. "Phylogeny and palaeoecology of Polyommatus blue butterflies show Beringia was a climate-regulated gateway to the New World." Proceedings of the Royal Society B: Biological Sciences 278, no. 1719 (2011): 2737–44. http://dx.doi.org/10.1098/rspb.2010.2213.

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Transcontinental dispersals by organisms usually represent improbable events that constitute a major challenge for biogeographers. By integrating molecular phylogeny, historical biogeography and palaeoecology, we test a bold hypothesis proposed by Vladimir Nabokov regarding the origin of Neotropical Polyommatus blue butterflies, and show that Beringia has served as a biological corridor for the dispersal of these insects from Asia into the New World. We present a novel method to estimate ancestral temperature tolerances using distribution range limits of extant organisms, and find that climati

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Olori, Jennifer C. "Ontogenetic sequence reconstruction and sequence polymorphism in extinct taxa: an example using early tetrapods (Tetrapoda: Lepospondyli)." Paleobiology 39, no. 3 (2013): 400–428. http://dx.doi.org/10.1666/12031.

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Ontogenetic sequence reconstruction is challenging particularly for extinct taxa because of when, where, and how fossils preserve. Different methods of reconstruction exist, but the effects of preservational bias, the applicability of size-independent methods, and the prevalence of sequence polymorphism (intraspecific variation) remain unexplored for paleontological data. Here I compare five different methods of ontogenetic sequence reconstruction and their effects on the detection of sequence polymorphism, using a large collection of the extinct vertebrates Microbrachis pelikani and Hyloplesi

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Springer, Mark S., Robert W. Meredith, Jan E. Janecka, and William J. Murphy. "The historical biogeography of Mammalia." Philosophical Transactions of the Royal Society B: Biological Sciences 366, no. 1577 (2011): 2478–502. http://dx.doi.org/10.1098/rstb.2011.0023.

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Palaeobiogeographic reconstructions are underpinned by phylogenies, divergence times and ancestral area reconstructions, which together yield ancestral area chronograms that provide a basis for proposing and testing hypotheses of dispersal and vicariance. Methods for area coding include multi-state coding with a single character, binary coding with multiple characters and string coding. Ancestral reconstruction methods are divided into parsimony versus Bayesian/likelihood approaches. We compared nine methods for reconstructing ancestral areas for placental mammals. Ambiguous reconstructions we

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Marchán, Daniel Fernández, Rosa Fernández, Irene de Sosa, Nuria Sánchez, Darío J. Díaz Cosín, and Marta Novo. "Integrative systematic revision of a Mediterranean earthworm family: Hormogastridae (Annelida, Oligochaeta)." Invertebrate Systematics 32, no. 3 (2018): 652. http://dx.doi.org/10.1071/is17048.

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The problem of reconciling earthworm taxonomy and phylogeny has shown advances with the application of molecular techniques, yet they have proven insufficient. Integrative systematics could solve this by combining multiple sources of evolutionary information. Relatively low diversity, restricted range and low nomenclatural conflict make Hormogastridae Michaelsen, 1900 a desirable target for an integrative systematics approach. The main systematic conflicts within this family are the polyphyly of the species Hormogaster pretiosa Michaelsen, 1899, the widespread presence of cryptic lineages, the

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Sherafati, Mahboubeh, Shahrokh Kazempour-Osaloo, Maryam Khoshsokhan-Mozaffar, Shokouh Esmailbegi Kermani, Yannick M. Staedler, and Sara Manafzadeh. "Diversification of Cynoglossinae genera (Cynoglosseae-Boraginaceae) in the western Irano–Turanian bioregion." Botany 99, no. 9 (2021): 541–53. http://dx.doi.org/10.1139/cjb-2020-0224.

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The Irano–Turanian (I–T) bioregion harbours one of the Old World’s greatest repositories of botanical diversity; however, the diversification patterns and the phenotypic evolution of its flora are sorely understudied. The subtribe Cynoglossinae is characteristic of the western I–T bioregion, species-rich in both the desertic lowlands and the more mesic highlands of the Iranian plateau. About 70 species of Cynoglossinae are present in the Iranian plateau, 47 of which are endemic to the plateau. Herein, nuclear internal transcribed spacer sequences as well as cpDNA rpl32-trnL and trnH–psbA seque

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Shirazinejad, Maliheh Pirayesh, Mansour Aliabadian, and Omid Mirshamsi. "The evolutionary history of the white wagtail species complex, (Passeriformes: Motacillidae: Motacilla alba)." Contributions to Zoology 88, no. 3 (2019): 257–76. http://dx.doi.org/10.1163/18759866-20191404.

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The white wagtail (Motacilla alba) species complex with its distinctive plumage in separate geographical areas can serve as a model to test evolutionary hypotheses. Its extensive variety in plumage, despite the genetic similarity between taxa, and the evolutionary events connected to this variety are poorly understood. Therefore we sampled in the breeding range of the white wagtail: 338 individuals were analyzed from 74 areas in the Palearctic and Mediterranean. We studied the white wagtail complex based on two mitochondrial DNA markers to make inferences about the evolutionary history. Our ph

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Abel, Christoph, Jutta M. Schneider, Matjaž Kuntner, and Danilo Harms. "Phylogeography of the ‘cosmopolitan’ orb-weaver Argiope trifasciata (Araneae: Araneidae)." Biological Journal of the Linnean Society 131, no. 1 (2020): 61–75. http://dx.doi.org/10.1093/biolinnean/blaa078.

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Abstract Few spider species show truly cosmopolitan distributions. Among them is the banded garden spider Argiope trifasciata, which is reported from six continents across major climatic gradients and geographical boundaries. In orb-weaver spiders, such global distributions might be a result of lively dispersal via ballooning. However, wide distributions might also be artefactual, owing to our limited understanding of species taxonomy. To test the hypothesis that A. trifasciata might be a complex of cryptic species with more limited geographical ranges, we investigated the biogeographical stru

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CADENA-CASTAÑEDA, OSCAR J., DIEGO MATHEUS DE MELLO MENDES, DANIELA SANTOS MARTINS SILVA, JUAN MANUEL CARDONA GRANDA, ALEXANDER GARCÍA GARCÍA, and JOSEF TUMBRINCK. "Systematics and biogeography of the genus Scaria Bolívar, 1887 (Orthoptera: Tetrigidae: Batrachideinae)." Zootaxa 4675, no. 1 (2019): 1–65. http://dx.doi.org/10.11646/zootaxa.4675.1.1.

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The Amazon rainforest is the world’s most extensive tropical rainforest, holding a considerable ecological and taxonomic diversity. Speciation in this region arises from multiple factors, such as topography, climate fluctuations, oceanic transgression, vegetation and the delimitation of zones circumscribed by sub-basins within the greater Amazon basin. Different scenarios have been proposed to better understand the diversification of Amazonian taxa, whether by Pleistocene refugia or by areas of endemism. The genus Scaria is distributed mostly in Amazonia, with a single species that ranges from

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Svenson, Gavin J., and Henrique M. Rodrigues. "A Cretaceous-aged Palaeotropical dispersal established an endemic lineage of Caribbean praying mantises." Proceedings of the Royal Society B: Biological Sciences 284, no. 1863 (2017): 20171280. http://dx.doi.org/10.1098/rspb.2017.1280.

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Recent phylogenetic advances have uncovered remarkable biogeographic histories that have challenged traditional concepts of dispersal, vicariance and diversification in the Greater Antilles. Much of this focus has centred on vertebrate lineages despite the high diversity and endemism of terrestrial arthropods, which account for 2.5 times the generic endemism of all Antillean plants and non-marine vertebrates combined. In this study, we focus on three Antillean endemic praying mantis genera, Callimantis , Epaphrodita and Gonatista , to determine their phylogenetic placement and geographical ori

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Agarwal, Ishan, Luis M. P. Ceríaco, Margarita Metallinou, Todd R. Jackman, and Aaron M. Bauer. "How the African house gecko ( Hemidactylus mabouia ) conquered the world." Royal Society Open Science 8, no. 8 (2021): 210749. http://dx.doi.org/10.1098/rsos.210749.

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Alien species are among the greatest threats to biodiversity, but the evolutionary origins of invasiveness remain obscure. We conducted the first range-wide sampling of Hemidactylus mabouia from more than 120 localities across Africa, Madagascar and the Neotropics to understand the evolutionary history of one of the most widely distributed, invasive vertebrates in the world. We used a multi-locus phylogeny, species delimitation, fossil-calibrated timetree, ancestral area reconstruction and species distribution models (SDMs) to determine how many putative species-level lineages are contained wi

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Bastide, Paul, Claudia Solís-Lemus, Ricardo Kriebel, K. William Sparks, and Cécile Ané. "Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations." Systematic Biology 67, no. 5 (2018): 800–820. http://dx.doi.org/10.1093/sysbio/syy033.

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Abstract The goal of phylogenetic comparative methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species’ traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to network

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Lima, Francoise D., Jan M. Strugnell, Tatiana S. Leite, and Sergio M. Q. Lima. "A biogeographic framework of octopod species diversification: the role of the Isthmus of Panama." PeerJ 8 (March 27, 2020): e8691. http://dx.doi.org/10.7717/peerj.8691.

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The uplift of the Isthmus of Panama (IP) created a land bridge between Central and South America and caused the separation of the Western Atlantic and Eastern Pacific oceans, resulting in profound changes in the environmental and oceanographic conditions. To evaluate how these changes have influenced speciation processes in octopods, fragments of two mitochondrial (Cytochrome oxidase subunit I, COI and 16S rDNA) and two nuclear (Rhodopsin and Elongation Factor-1α, EF-1α) genes were amplified from samples from the Atlantic and Pacific oceans. One biogeographical and four fossil calibration prio

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Urbaniak, Monika, Agnieszka Waśkiewicz, Artur Trzebny, Grzegorz Koczyk, and Łukasz Stępień. "Cyclodepsipeptide Biosynthesis in Hypocreales Fungi and Sequence Divergence of The Non-Ribosomal Peptide Synthase Genes." Pathogens 9, no. 7 (2020): 552. http://dx.doi.org/10.3390/pathogens9070552.

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Fungi from the Hypocreales order synthesize a range of toxic non-ribosomal cyclic peptides with antimicrobial, insecticidal and cytotoxic activities. Entomopathogenic Beauveria, Isaria and Cordyceps as well as phytopathogenic Fusarium spp. are known producers of beauvericins (BEAs), beauvenniatins (BEAEs) or enniatins (ENNs). The compounds are synthesized by beauvericin/enniatin synthase (BEAS/ESYN1), which shows significant sequence divergence among Hypocreales members. We investigated ENN, BEA and BEAE production among entomopathogenic (Beauveria, Cordyceps, Isaria) and phytopathogenic (Fusa

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Worsaae, Katrine, Gonzalo Giribet, and Alejandro Martínez. "The role of progenesis in the diversification of the interstitial annelid lineage Psammodrilidae." Invertebrate Systematics 32, no. 4 (2018): 774. http://dx.doi.org/10.1071/is17063.

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Psammodrilidae constitutes a family of understudied, nearly completely ciliated, small-sized annelids, whose systematic position in Annelida remains unsettled and whose internal phylogeny is here investigated for the first time. Psammodrilids possess hooked chaetae typical of macroscopic tube-dwelling semi-sessile annelids, such as Arenicolidae. Yet, several minute members resemble, with their conspicuous gliding by ciliary motion and vagile lifestyle, interstitial fauna, adapted to move between sand grains. Moreover, psammodrilids exhibit a range of unique features, for example, bendable acic

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Sumarto, Bayu K. A., Hirozumi Kobayashi, Ryo Kakioka, et al. "Latitudinal variation in sexual dimorphism in a freshwater fish group." Biological Journal of the Linnean Society 131, no. 4 (2020): 898–908. http://dx.doi.org/10.1093/biolinnean/blaa166.

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Abstract Tropical animals are characterized by showy ornaments and conspicuous body colours as compared with their temperate relatives. Some recent studies have hypothesized that sexual selection pressures are stronger in the tropics than in the temperate zone. Although negative correlations between latitude and the degree of sexual dimorphism would support this hypothesis, phylogeny should be taken into account in such comparative studies. Comparisons of the degree of sexual dimorphism in body size and fin lengths among species of the Adrianichthyidae, a freshwater fish family having a wide g

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Richmond, Jonathan Q., Hidetoshi Ota, L. Lee Grismer, and Robert N. Fisher. "Influence of niche breadth and position on the historical biogeography of seafaring scincid lizards." Biological Journal of the Linnean Society 132, no. 1 (2020): 74–92. http://dx.doi.org/10.1093/biolinnean/blaa172.

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Abstract Niche breadth and position can influence diversification among closely related species or populations, yet limited empirical data exist concerning the predictability of the outcomes. We explored the effects of these factors on the evolution of the Emoia atrocostata species group, an insular radiation of lizards in the western Pacific Ocean and Indo-Australasia composed of both endemic and widespread species that differ in niche occupancy. We used molecular data and phylogeographical diffusion models to estimate the timing and patterns of range expansion, and ancestral reconstruction m

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Harrison, Peter W., Alison E. Wright, Fabian Zimmer, et al. "Sexual selection drives evolution and rapid turnover of male gene expression." Proceedings of the National Academy of Sciences 112, no. 14 (2015): 4393–98. http://dx.doi.org/10.1073/pnas.1501339112.

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The profound and pervasive differences in gene expression observed between males and females, and the unique evolutionary properties of these genes in many species, have led to the widespread assumption that they are the product of sexual selection and sexual conflict. However, we still lack a clear understanding of the connection between sexual selection and transcriptional dimorphism, often termed sex-biased gene expression. Moreover, the relative contribution of sexual selection vs. drift in shaping broad patterns of expression, divergence, and polymorphism remains unknown. To assess the ro

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Farji-Brener, Alejandro G., Luciana Elizalde, Hermógenes Fernández-Marín, and Sabrina Amador-Vargas. "Social life and sanitary risks: evolutionary and current ecological conditions determine waste management in leaf-cutting ants." Proceedings of the Royal Society B: Biological Sciences 283, no. 1831 (2016): 20160625. http://dx.doi.org/10.1098/rspb.2016.0625.

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Adequate waste management is vital for the success of social life, because waste accumulation increases sanitary risks in dense societies. We explored why different leaf-cutting ants (LCA) species locate their waste in internal nest chambers or external piles, including ecological context and accounting for phylogenetic relations. We propose that waste location depends on whether the environmental conditions enhance or reduce the risk of infection. We obtained the geographical range, habitat and refuse location of LCA from published literature, and experimentally determined whether pathogens o

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Dacks, Joel B., and W. Ford Doolittle. "Novel syntaxin gene sequences from Giardia, Trypanosoma and algae: implications for the ancient evolution of the eukaryotic endomembrane system." Journal of Cell Science 115, no. 8 (2002): 1635–42. http://dx.doi.org/10.1242/jcs.115.8.1635.

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SNAP receptors or SNARES are crucial components of the intracellular membrane system of eukaryotes. The syntaxin family of SNAREs have been shown to have roles in neurotransmission, vesicular transport, membrane fusion and even internal membrane compartment reconstruction. While syntaxins and SNAREs in general have been well characterized in mammalian and yeast models, little is known about their overall distribution across eukaryotic diversity or about the evolution of the syntaxin gene family. By combining bioinformatic,molecular biological and phylogenetic approaches, we demonstrate that va

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Du Pasquier, Pierre-Emmanuel, Daniel Jeanmonod, and Yamama Naciri. "Morphological convergence in the recently diversified Silene gigantea complex (Caryophyllaceae) in the Balkan Peninsula and south-western Turkey, with the description of a new subspecies." Botanical Journal of the Linnean Society 183, no. 3 (2017): 474–93. http://dx.doi.org/10.1093/botlinnean/bow016.

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Abstract The Silene gigantea complex is characterized by a high degree of morphological variability that resulted in the description of three subspecies across its distribution range from the Balkan Peninsula to South-west Asia and Cyprus. In this work, we used nuclear and plastid markers in Bayesian phylogeographic analyses to investigate the taxonomy and the evolutionary history of S. gigantea. The results from plastid DNA partly support the existing taxonomic assessments since S. gigantea subsp. rhodopea is monophyletic, whereas S. gigantea subspp. gigantea and hellenica are clearly polyphy

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LAMM, Kristin S., and Benjamin D. REDELINGS. "Reconstructing ancestral ranges in historical biogeography: properties and prospects." Journal of Systematics and Evolution 47, no. 5 (2009): 369–82. http://dx.doi.org/10.1111/j.1759-6831.2009.00042.x.

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Griffin, Christopher T., and Kenneth D. Angielczyk. "The evolution of the dicynodont sacrum: constraint and innovation in the synapsid axial column." Paleobiology 45, no. 1 (2019): 201–20. http://dx.doi.org/10.1017/pab.2018.49.

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AbstractConstraint is a universal feature of morphological evolution. The vertebral column of synapsids (mammals and their close relatives) is a classic example of this phenotypic restriction, with greatly reduced variation in the number of vertebrae compared with the sauropsid lineage. Synapsids generally possess only three sacral vertebrae, which articulate with the ilium and play a key role in locomotion. Dicynodont anomodonts are the exception to this rule, possessing seven or more sacral vertebrae while reaching a range of body sizes rivaled among synapsids only by therian mammals. Here w

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Gamba-Moreno, Diana Lucia, and Frank Almeda. "Systematics of the Octopleura Clade of Miconia (Melastomataceae: Miconieae) in Tropical America." Phytotaxa 179, no. 1 (2014): 1. http://dx.doi.org/10.11646/phytotaxa.179.1.1.

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The Octopleura clade of Miconia is a natural group of Neotropical subshrubs and small trees comprising some thirty-three species. These had previously been described in Ossaea and Clidemia, two traditionally recognized genera of Miconieae, but this natural group is nested within the megadiverse genus Miconia. This study represents the first comprehensive monograph of the clade across its entire range based on a study of over 2100 collections from seven herbaria. Thirteen new combinations are made (Miconia aguilarii, M. aurantiaca, M. biolleyana, M. boekei, M. chocoensis, M. evanescens, M. ince

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Robinson, Serina L., Barbara R. Terlouw, Megan D. Smith та ін. "Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia". Journal of Biological Chemistry 295, № 44 (2020): 14826–39. http://dx.doi.org/10.1074/jbc.ra120.013528.

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Enzymes that cleave ATP to activate carboxylic acids play essential roles in primary and secondary metabolism in all domains of life. Class I adenylate-forming enzymes share a conserved structural fold but act on a wide range of substrates to catalyze reactions involved in bioluminescence, nonribosomal peptide biosynthesis, fatty acid activation, and β-lactone formation. Despite their metabolic importance, the substrates and functions of the vast majority of adenylate-forming enzymes are unknown without tools available to accurately predict them. Given the crucial roles of adenylate-forming en

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Badik, Kevin J., Joshua P. Jahner, and Joseph S. Wilson. "A biogeographic perspective on the evolution of fire syndromes in pine trees ( Pinus : Pinaceae)." Royal Society Open Science 5, no. 3 (2018): 172412. http://dx.doi.org/10.1098/rsos.172412.

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Our goals were to explore the relationship between biogeography and the evolution of fire-adaptive syndromes in the genus Pinus . We used a previously published time-calibrated phylogeny and conducted ancestral trait reconstruction to estimate the likely timing of diversification in Pinus , and to determine when fire-adaptive syndromes evolved in the lineage. To explore trait conservation among fire syndromes and to investigate historical biogeography, we constructed ancestral state reconstructions using the program RASP and estimated the degree of conservatism for fire-adapted traits in the p

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Yang, Z., S. Kumar, and M. Nei. "A new method of inference of ancestral nucleotide and amino acid sequences." Genetics 141, no. 4 (1995): 1641–50. http://dx.doi.org/10.1093/genetics/141.4.1641.

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Abstract A statistical method was developed for reconstructing the nucleotide or amino acid sequences of extinct ancestors, given the phylogeny and sequences of the extant species. A model of nucleotide or amino acid substitution was employed to analyze data of the present-day sequences, and maximum likelihood estimates of parameters such as branch lengths were used to compare the posterior probabilities of assignments of character states (nucleotides or amino acids) to interior nodes of the tree; the assignment having the highest probability was the best reconstruction at the site. The lysozy

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Outlaw, Diana C., Gary Voelker, Borja Mila, and Derek J. Girman. "Evolution of Long-Distance Migration in and Historical Biogeography of Catharus Thrushes: A Molecular Phylogenetic Approach." Auk 120, no. 2 (2003): 299–310. http://dx.doi.org/10.1093/auk/120.2.299.

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Abstract We addressed the evolution of long-distance migration in and the historical biogeography of Catharus thrushes within a phylogenetic framework. Catharus thrushes are a Nearctic–Neotropical genus consisting of five migrant and seven resident species. We reconstructed a molecular phylogeny using a combined analysis of cytochrome-b and ND2 genes. Phylogenetic reconstructions indicate the nonmonophyly of migratory Catharus species. The Neotropics are the most likely ancestral geographic area for the entire lineage, and migratory species are sister to resident taxa whose ranges are restrict

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Vidya, T. N. C., Raman Sukumar, and Don J. Melnick. "Range-wide mtDNA phylogeography yields insights into the origins of Asian elephants." Proceedings of the Royal Society B: Biological Sciences 276, no. 1658 (2008): 893–902. http://dx.doi.org/10.1098/rspb.2008.1494.

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Recent phylogeographic studies of the endangered Asian elephant ( Elephas maximus ) reveal two highly divergent mitochondrial DNA (mtDNA) lineages, an elucidation of which is central to understanding the species's evolution. Previous explanations for the divergent clades include introgression of mtDNA haplotypes between ancestral species, allopatric divergence of the clades between Sri Lanka or the Sunda region and the mainland, historical trade of elephants, and retention of divergent lineages due to large population sizes. However, these studies lacked data from India and Myanmar, which host

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Zuluaga, Alejandro, Martin Llano, and Ken Cameron. "Systematics, Biogeography, and Morphological Character Evolution of the Hemiepiphytic Subfamily Monsteroideae (Araceae)." Annals of the Missouri Botanical Garden 104, no. 1 (2019): 33–48. http://dx.doi.org/10.3417/2018269.

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The subfamily Monsteroideae (Araceae) is the third richest clade in the family, with ca. 369 described species and ca. 700 estimated. It comprises mostly hemiepiphytic or epiphytic plants restricted to the tropics, with three intercontinental disjunctions. Using a dataset representing all 12 genera in Monsteroideae (126 taxa), and five plastid and two nuclear markers, we studied the systematics and historical biogeography of the group. We found high support for the monophyly of the three major clades (Spathiphylleae sister to Heteropsis Kunth and Rhaphidophora Hassk. clades), and for six of th

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Rahman, Imran A., Samuel Zamora, Peter L. Falkingham, and Jeremy C. Phillips. "Cambrian cinctan echinoderms shed light on feeding in the ancestral deuterostome." Proceedings of the Royal Society B: Biological Sciences 282, no. 1818 (2015): 20151964. http://dx.doi.org/10.1098/rspb.2015.1964.

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Reconstructing the feeding mode of the latest common ancestor of deuterostomes is key to elucidating the early evolution of feeding in chordates and allied phyla; however, it is debated whether the ancestral deuterostome was a tentaculate feeder or a pharyngeal filter feeder. To address this, we evaluated the hydrodynamics of feeding in a group of fossil stem-group echinoderms (cinctans) using computational fluid dynamics. We simulated water flow past three-dimensional digital models of a Cambrian fossil cinctan in a range of possible life positions, adopting both passive tentacular feeding an

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Misiewicz, T. M., and N. C. Zerega. "PHYLOGENY, BIOGEOGRAPHY AND CHARACTER EVOLUTION OF DORSTENIA (MORACEAE)." Edinburgh Journal of Botany 69, no. 3 (2012): 413–40. http://dx.doi.org/10.1017/s096042861200025x.

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Dorstenia, the second largest genus (105 species) within the Moraceae, is the only genus in the family with woody, herbaceous and succulent species. All but one species of Dorstenia are restricted to the Neotropics or Africa, and it is the only genus in the family with an almost equal transatlantic distribution. This work presents the first molecular phylogeny and the first evolutionary study to examine origin and diversification within the genus. We inferred the phylogeny with ITS sequence data using Bayesian and maximum likelihood approaches. We tracked the evolution of distinct morphologica

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Holterman, M., G. Karssen, S. van den Elsen, H. van Megen, J. Bakker, and J. Helder. "Small Subunit rDNA-Based Phylogeny of the Tylenchida Sheds Light on Relationships Among Some High-Impact Plant-Parasitic Nematodes and the Evolution of Plant Feeding." Phytopathology® 99, no. 3 (2009): 227–35. http://dx.doi.org/10.1094/phyto-99-3-0227.

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Cyst (Heteroderidae), root knot (Meloidogyne spp.), and lesion (Pratylenchus spp.) nematodes all belong to a single nematode order, Tylenchida. However, the relationships between and within these economically highly relevant groups, and their relatedness to other parasitic Tylenchida is unclear. We constructed a phylogeny of 116 Tylenchida taxa based on full length small subunit ribosomal DNA (small subunit [SSU] rDNA) sequences. Ancestral state reconstruction points at a gradual development of simple to more complex forms of plant parasitism. Good resolution was observed in distal clades that

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Aliev, Chabagin U., Anastasia M. Koltunova, Maxim G. Kutsev, and Boris S. Tuniyev. "Population genetic analysis of Fagus orientalis Lipsky from the territory of the Crimea and the Caucasus." Turczaninowia 23, no. 4 (2020): 17–31. http://dx.doi.org/10.14258/turczaninowia.23.4.3.

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The genetic structure of 20 populations of Fagus orientalis Lipsky (oriental beech) from the territory of the Crimea and the Caucasus was studied on the basis of microsatellite polymorphism (SSR – simple sequence repeats). The isolation distance test performed in the GenePop program showed a high correlation of genetic differences and the logarithm of geographic distance in geographic coordinates at the 0.91 level. Interpopulation genetic differentiation of Fagus orientalis (Fst) ranged from 0.01 to 0.67. On the basis of the obtained genetic data and analysis of the literature on fossil materi

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