Recent origin of Neotropical orchids in the world’s richest plant biodiversity hotspot

Abstract• The Andean mountains of South America are the most species-rich biodiversity hotspot worldwide with about 15% of the world’s plant species, in only 1% of the world’s land surface. Orchids are a key element of the Andean flora, and one of the most prominent components of the Neotropical epiphyte diversity, yet very little is known about their origin and diversification.• We address this knowledge gap by inferring the biogeographical history and evolutionary dynamics of the two largest Neotropical orchid groups (Cymbidieae and Pleurothallidinae), using two unparalleled, densely-sampled orchid phylogenies (including 400+ newly generated DNA sequences), comparative phylogenetic methods, geological and biological datasets.• We find that the majority of Andean orchid lineages only originated in the last 15 million years. Most Andean lineages are derived from lowland Amazonian ancestors, with additional contributions from Central America and the Antilles. Species diversification is correlated with Andean orogeny, and multiple migrations and re-colonizations across the Andes indicate that mountains do not constrain orchid dispersal over long timescales.• Our study sheds new light on the timing and geography of a major Neotropical radiation, and suggests that mountain uplift promotes species diversification across all elevational zones.

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Evolutionary dynamics of neutral phenotypes under DNA substitution models

10.1101/2020.10.26.355438 ◽

2020 ◽

Author(s):

Shadi Zabad ◽

Alan M Moses

Keyword(s):

Dna Sequences ◽

Evolutionary Dynamics ◽

Gc Content ◽

Stabilizing Selection ◽

Restoring Force ◽

Dna Substitution ◽

Long Term Trends ◽

The Mean ◽

Molecular Phenotypes

AbstractWe study the evolution of quantitative molecular traits in the absence of selection. Using a simple theory based on Felsenstein’s 1981 DNA substitution model, we predict a linear restoring force on the mean of an additive phenotype. Remarkably, the mean dynamics are independent of the effect sizes and genotype and are similar to the widely-used OU model for stabilizing selection. We confirm the predictions empirically using additive molecular phenotypes calculated from ancestral reconstructions of putatively unconstrained DNA sequences in primate genomes. We show that the OU model is favoured by inference software even when applied to GC content of unconstrained sequences or simulations of DNA evolution. We predict and confirm empirically that the dynamics of the variance are more complicated than those predicted by the OU model, and show that our results for the restoring force of mutation hold even for non-additive phenotypes, such as number of transcription factor binding sites, longest encoded peptide and folding propensity of the encoded peptide. Our results have implications for efforts to infer selection based on quantitative phenotype dynamics as well as to understand long-term trends in evolution of quantitative molecular traits.

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Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

10.1101/210955 ◽

2017 ◽

Cited By ~ 10

Author(s):

Nandita R. Garud ◽

Benjamin H. Good ◽

Oskar Hallatschek ◽

Katherine S. Pollard

Keyword(s):

Evolutionary Dynamics ◽

Purifying Selection ◽

Gut Bacteria ◽

Fundamental Limits ◽

Evolutionary Forces ◽

Standard Population ◽

Evolutionary Changes ◽

Or Gene ◽

Adult Twins ◽

Long Timescales

AbstractGut microbiota are shaped by a combination of ecological and evolutionary forces. While the ecological dynamics have been extensively studied, much less is known about how species of gut bacteria evolve over time. Here we introduce a model-based framework for quantifying evolutionary dynamics within and across hosts using a panel of metagenomic samples. We use this approach to study evolution in ∼30 prevalent species in the human gut. Although the patterns of between-host diversity are consistent with quasi-sexual evolution and purifying selection on long timescales, we identify new genealogical signatures that challenge standard population genetic models of these processes. Within hosts, we find that genetic differences that accumulate over ∼6 month timescales are only rarely attributable to replacement by distantly related strains. Instead, the resident strains more commonly acquire a smaller number of putative evolutionary changes, in which nucleotide variants or gene gains or losses rapidly sweep to high frequency. By comparing these mutations with the typical between-host differences, we find evidence that some sweeps are seeded by recombination, in addition to new mutations. However, comparisons of adult twins suggest that replacement eventually overwhelms evolution over multi-decade timescales, hinting at fundamental limits to the extent of local adaptation. Together, our results suggest that gut bacteria can evolve on human-relevant timescales, and they highlight the connections between these short-term evolutionary dynamics and longer-term evolution across hosts.

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A revision of Onychelmis Hinton, 1941 (Coleoptera: Elmidae), with description of new species, DNA barcoding and notes on the geography of the genus

European Journal of Taxonomy ◽

10.5852/ejt.2021.739.1263 ◽

2021 ◽

Vol 739 ◽

pp. 1-35

Author(s):

Marek Linský ◽

Zuzana Čiamporová-Zaťovičová ◽

Fedor Čiampor Jr

Keyword(s):

New Species ◽

Dna Sequences ◽

Species Delimitation ◽

Molecular Data ◽

Distribution Map ◽

Line Drawings ◽

The Andes ◽

Long Time ◽

New Material ◽

Morphological And Molecular Data

The genus Onychelmis Hinton, 1941 was for a long time regarded as a small taxon with only three known species distributed in the Andes. A study of new material from Ecuador, using morphological and molecular data, has resulted in the discovery of five new species: Onychelmis lenkae sp. nov., O. lobata sp. nov., O. minor sp. nov., O. onorei sp. nov. and O. splendida sp. nov. We also revised the entire genus and redescribed the three known species, O. longicollis (Sharp, 1882), O. leleupi Delève, 1968 and O. whiteheadi Spangler & Santiago, 1991. Habitus photographs of adults are provided, together with line drawings of male and female genitalia, and schematic illustrations of the distribution of femoral tomentum for each species. DNA sequences for barcoding the COI mtDNA fragment were used to support species delimitation and to suggest possible relationships among species. The revision includes a key to adults of all species of Onychelmis and notes on the biogeography of the genus, with an updated distribution map.

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An ABBA-BABA Test for Introgression Using Retroposon Insertion Data

10.1101/709477 ◽

2019 ◽

Cited By ~ 2

Author(s):

Mark S. Springer ◽

John Gatesy

Keyword(s):

Dna Sequences ◽

Incomplete Lineage Sorting ◽

Species Tree ◽

Data Sets ◽

Lineage Sorting ◽

Sequence Alignments ◽

Data Set ◽

Short Branch ◽

Phylogenetic Methods ◽

Branch Lengths

AbstractDNA sequence alignments provide the majority of data for inferring phylogenetic relationships with both concatenation and coalescence methods. However, DNA sequences are susceptible to extensive homoplasy, especially for deep divergences in the Tree of Life. Retroposon insertions have emerged as a powerful alternative to sequences for deciphering evolutionary relationships because these data are nearly homoplasy-free. In addition, retroposon insertions satisfy the ‘no intralocus recombination’ assumption of summary coalescence methods because they are singular events and better approximate neutrality relative to DNA sequences commonly applied in phylogenomic work. Retroposons have traditionally been analyzed with phylogenetic methods that ignore incomplete lineage sorting (ILS). Here, we analyze three retroposon data sets for mammals (Placentalia, Laurasiatheria, Balaenopteroidea) with two different ILS-aware methods. The first approach constructs a species tree from retroposon bipartitions with ASTRAL, and the second is a modification of SVD-Quartets. We also develop a χ2 Quartet-Asymmetry Test to detect hybridization using retroposon data. Both coalescence methods recovered the same topology for each of the three data sets. The ASTRAL species tree for Laurasiatheria has consecutive short branch lengths that are consistent with an anomaly zone situation. For the Balaenopteroidea data set, which includes rorquals (Balaenopteridae) and gray whale (Eschrichtiidae), both coalescence methods recovered a topology that supports the paraphyly of Balaenopteridae. Application of the χ2 Quartet-Asymmetry Test to this data set detected 16 different quartets of species for which historical hybridization may be inferred, but significant asymmetry was not detected in the placental root and Laurasiatheria analyses.

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Cryptic fungal species unmasked

Microbiology Australia ◽

10.1071/ma12036 ◽

2012 ◽

Vol 33 (1) ◽

pp. 36 ◽

Cited By ~ 9

Author(s):

Roger G Shivas ◽

Lei Cai

Keyword(s):

Host Range ◽

Cryptic Species ◽

Geographic Distribution ◽

Dna Sequences ◽

Fungal Species ◽

Phylogenetic Methods ◽

Molecular Phylogenetic

The word cryptic is derived from the Greek adjective krupt�s which means hidden. Morphologically indistinguishable species that have been revealed by molecular phylogenetic methods, and 37ultimately only recognised by their DNA sequences, are referred to as cryptic species. The importance of cryptic species for plant pathologists is that they may have significant differences in the severity of diseases they cause, host range and geographic distribution. It is these differences that are of concern to many biosecurity agencies, particularly in Australia.

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Mode and Tempo of Microsatellite Evolution across 300 Million Years of Insect Evolution

Genes ◽

10.3390/genes11080945 ◽

2020 ◽

Vol 11 (8) ◽

pp. 945

Author(s):

Michelle Jonika ◽

Johnathan Lo ◽

Heath Blackmon

Keyword(s):

Chromosome Number ◽

Dna Sequences ◽

Evolutionary Dynamics ◽

Genome Structure ◽

Holocentric Chromosomes ◽

Repetitive Dna Sequences ◽

Chromosome Type ◽

Assembly Quality ◽

Microsatellite Evolution ◽

The Impact

Microsatellites are short, repetitive DNA sequences that can rapidly expand and contract due to slippage during DNA replication. Despite their impacts on transcription, genome structure, and disease, relatively little is known about the evolutionary dynamics of these short sequences across long evolutionary periods. To address this gap in our knowledge, we performed comparative analyses of 304 available insect genomes. We investigated the impact of sequence assembly methods and assembly quality on the inference of microsatellite content, and we explored the influence of chromosome type and number on the tempo and mode of microsatellite evolution across one of the most speciose clades on the planet. Diploid chromosome number had no impact on the rate of microsatellite evolution or the amount of microsatellite content in genomes. We found that centromere type (holocentric or monocentric) is not associated with a difference in the amount of microsatellite content; however, in those species with monocentric chromosomes, microsatellite content tends to evolve faster than in species with holocentric chromosomes.

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Exploring the 36Cl/Cl input in arid environments: New insights gained by 81Kr groundwater dating in the Negev Desert, Israel

10.5194/egusphere-egu21-4143 ◽

2021 ◽

Author(s):

Roi Ram ◽

Roland Purtschert ◽

Christof Vockenhuber ◽

Reika Yokochi ◽

Eilon M. Adar ◽

...

Keyword(s):

Land Surface ◽

Noble Gas ◽

Climatic Conditions ◽

Arid Environments ◽

Near Surface ◽

Spatial Differences ◽

Practical Tool ◽

Groundwater Dating ◽

Long Timescales

&#160;&#160; 36Cl and 81Kr (half-lives of 301 and 229 kyr, respectively) are among a very few age tracers with dating capabilities in the 104&#8211;106 yr timescale. Although widely applied since the 1980s in various hydrological studies, the 36Cl/Cl system has been found complex as an effective dating tool. In contrast, 81Kr has become a practical tool only recently and is considered to be an ideal dating tool due to the inert properties of the noble gas. In the present study, simultaneous measurements of both radioisotopes were used to assess the 36Cl/Cl input ratios and the Cl- content for paleorecharge into the deep, transboundary Nubian Sandstone Aquifer (NSA) which stretches below the hyperarid deserts of the Sinai Peninsula (Egypt) and the Negev (Israel).&#160;&#160; By means of 81Kr data, reconstructed Cl- content of recharge that occurred during the late Pleistocene was found to be 300&#8211;400 mg/L with an initial 36Cl/Cl ratio of 50 &#215; 10-15. This latter value is in agreement with the 36Cl/Cl ratio in recent local rainwater, indicating constancy over prolonged periods with possible variable climatic conditions. This similarity in values suggests a process that is rather insensitive to atmospheric 36Cl fallout rates. Erosion and weathering of near-surface materials in the desert environment could dominate the hydrochemistry of rains, floods, and the consequent groundwater recharge. This near-surface Cl- reservoir integrates various sources and processes, including marine and terrestrial Cl-, cosmogenic 36Cl fallout, and cosmogenic 36Cl production in the shallow unsaturated zone, all of which are active over long timescales and accumulate on the land surface and in the epigene zone.&#160; Spatial differences in the reconstructed initial 36Cl/Cl ratio are attributed to differences in the mineral aerosol sources for specific recharge areas of the NSA. The results of this study highlight the potential of integrating 81Kr age information in evaluating the initial 36Cl/Cl and Cl- input, which is essential for the calibration of 36Cl radioisotope as a long-term dating tool for a given basin.

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Systematic considerations on two species of nectarivorous bats (Anoura caudifer and A. geoffroyi) based on barcoding sequences

Acta Biológica Colombiana ◽

10.15446/abc.v25n2.75848 ◽

2020 ◽

Vol 25 (2) ◽

pp. 194-201

Author(s):

Andrés Felipe Vargas Arboleda ◽

Sebastían Cuadrado-Rios ◽

Hugo Mantilla-Meluk

Keyword(s):

Dna Sequences ◽

Wide Distribution ◽

Central American ◽

Specific Level ◽

The Andes ◽

Isthmus Of Panama ◽

Geographic Structure ◽

Species Complexes ◽

The Pacific ◽

Ecological Complexity

As a product of recent revisions of the nectivore bat genus Anoura (Glossophaginae: Anourina), new species have been described, and several taxa have been elevated to the specific level in the so-called Anoura caudifer and A. geoffroyi species complexes in the last four decades. The genus has a wide distribution across regions of high ecological complexity, including geographic features, such as the Andes and the Isthmus of Panamá, previously identified as natural barriers that restrict gene flow in other phyllostomid bat genera. Up to date, no analyses have been conducted to investigate the contribution of biogeographic factors on the genetic divergence of the genus. In this work, we analyze barcoding DNA sequences (cytochrome oxidase subunit I, COI) to test for geographic structure among Central and South American populations of the A. caudifer and A. geoffroyi complexes. Our analyses show geographic structure for populations previously identified as the A. geoffroyi lasiopyga, suggesting an independent evolutionary fate for Central American representatives of the genus. We also highlight the presence of unrecognized diversity within the A. caudifer complex from the Pacific coast of northern Ecuador.

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Elevational Zonation and the Phylogenetic Relationships of the Henicorhina Wood-Wrens

The Auk ◽

10.1093/auk/123.1.119 ◽

2006 ◽

Vol 123 (1) ◽

pp. 119-134 ◽

Cited By ~ 4

Author(s):

Caroline Dingle ◽

Irby J. Lovette ◽

Chris Canaday ◽

Thomas B. Smith

Keyword(s):

Central America ◽

Dna Sequences ◽

Genetic Relationships ◽

Elevational Gradient ◽

Species Status ◽

Ecological Diversification ◽

Evolutionary Origins ◽

The Andes

Abstract The Henicorhina wood-wren complex consists of three taxonomic species. Two of these, the Gray-breasted Wood-Wren (Henicorhina leucophrys) and the White-breasted Wood-Wren (H. leucosticta), are widespread throughout Central America and northern South America, with leucophrys occurring at higher elevations in regions where both occur. A third, recently described, species—the Bar-winged Wood-Wren (H. leucoptera)—occurs only in several isolated cordilleras in southeastern Ecuador and northeastern Peru, where it replaces the Gray-breasted Wood-Wren at the highest elevations. We used mitochondrial DNA sequences to explore the phylo-genetic relationships among populations of these taxa and to draw inferences about the evolutionary origins of elevational zonation. We found substantial mitochondrial diversity within both leucophrys and leucosticta. Differentiation across the Andes in leucophrys was negligible, but populations from Central America and from northwestern Ecuador showed substantial differentiation. Three highly differentiated haplotype groups were also present in leucosticta, corresponding to populations in the eastern Andean lowlands, Central America, and the Chocó region of northwestern Ecuador; these populations may each warrant taxonomic species status. Bar-winged haplo-types nested within the mitochondrially diverse leucosticta group, where they were most closely allied to the geographically distant Chocó haplotypes. This leucoptera-leucosticta affinity is not consistent with previous inferences, based on plumage and behavioral similarities, that grouped leucoptera and leucophrys as sister species. These reconstructions refute the hypothesis that elevational zonation in this clade originated from in situ speciation along an elevational gradient, and instead highlight the role of complex changes in geographic distributions in fostering phylogenetic and ecological diversification. Reemplazos Altitudinales y Relaciones Filogenéticas en el Género Henicorhina (Troglodytidae)

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Inferring Diversity and Evolution in Fish by Means of Integrative Molecular Cytogenetics

The Scientific World JOURNAL ◽

10.1155/2015/365787 ◽

2015 ◽

Vol 2015 ◽

pp. 1-10 ◽

Cited By ~ 6

Author(s):

Roberto Ferreira Artoni ◽

Jonathan Pena Castro ◽

Uedson Pereira Jacobina ◽

Paulo Augusto Lima-Filho ◽

Gideão Wagner Werneck Félix da Costa ◽

...

Keyword(s):

Dna Sequences ◽

Evolutionary Biology ◽

Evolutionary Dynamics ◽

Biological Diversity ◽

Molecular Cytogenetics ◽

Structural Features ◽

Fish Chromosomes ◽

Population Structuring ◽

The Will

Fish constitute a paraphyletic and profusely diversified group that has historically puzzled ichthyologists. Hard efforts are necessary to better understand this group, due to its extensive diversity. New species are often identified and it leads to questions about their phylogenetic aspects. Cytogenetics is becoming an important biodiversity-detection tool also used to measure biodiversity evolutionary aspects. Molecular cytogenetics by fluorescencein situhybridization (FISH) allowed integrating quantitative and qualitative data from DNA sequences and their physical location in chromosomes and genomes. Although there is no intention on presenting a broader review, the current study presents some evidences on the need of integrating molecular cytogenetic data to other evolutionary biology tools to more precisely infer cryptic species detection, population structuring in marine environments, intra- and interspecific karyoevolutionary aspects of freshwater groups, evolutionary dynamics of marine fish chromosomes, and the origin and differentiation of sexual and B chromosomes. The new cytogenetic field, called cytogenomics, is spreading due to its capacity to give resolute answers to countless questions that cannot be answered by traditional methodologies. Indeed, the association between chromosomal markers and DNA sequencing as well as between biological diversity analysis methodologies and phylogenetics triggers the will to search for answers about fish evolutionary, taxonomic, and structural features.

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