Homology among RAPD fragments in interspecific comparisons

The use of RAPDs for comparative purposes relies on the assumption that similarity of fragment size is a dependable indicator of homology. To test the validity of this assumption, homology among 220 pairs of comigrating fragments from three wild sunflower species was determined. Ninety-one per cent cross-hybridized and/or displayed congruent restriction fragment profiles suggestive of homology. However, comparative linkage mapping data indicated that 13% of the homologous loci mapped to genomic locations that were incongruent with the majority of loci, suggestive of paralogous rather than orthologous relationships. Thus, of the 220 pairwise comparisons, only 174 (79.1%) identified loci that are useful for comparative genetic studies. These problems, as well as several other factors discussed in the text, will introduce noise into RAPD data sets and thereby reduce the probability of generating accurate estimates of genetic relationships. Recommended methods for reducing noise in RAPD data sets include increasing gel resolution and/or testing fragment homology. However, implementation of these approaches will not eliminate all uncertainties, and it is also recommended that RAPD data sets be tested for structure and reliability.     

Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.

The RADseq technology allows researchers to efficiently develop thousands of polymorphic loci across multiple individuals with little or no prior information on the genome. However, many questions remain about the biases inherent to this technology. Notably, sequence misalignments arising from paralogy may affect the development of single nucleotide polymorphism (SNP) markers and the estimation of genetic diversity. We evaluated the impact of putative paralog loci on genetic diversity estimation during the development of SNPs from a RADseq dataset for the nonmodel tree species Robinia pseudoacacia L. We sequenced nine genotypes and analyzed the frequency of putative paralogous RAD loci as a function of both the depth of coverage and the mismatch threshold allowed between loci. Putative paralogy was detected in a very variable number of loci, from 1% to more than 20%, with the depth of coverage having a major influence on the result. Putative paralogy artificially increased the observed degree of polymorphism and resulting estimates of diversity. The choice of the depth of coverage also affected diversity estimation and SNP validation: A low threshold decreased the chances of detecting minor alleles while a high threshold increased allelic dropout. SNP validation was better for the low threshold (4×) than for the high threshold (18×) we tested. Using the strategy developed here, we were able to validate more than 80% of the SNPs tested by means of individual genotyping, resulting in a readily usable set of 330 SNPs, suitable for use in population genetics applications.     

Evolution of duplicated alpha-tubulin genes in ciliates

Ciliates provide a powerful system to analyze the evolution of duplicated alpha-tubulin genes in the context of single-celled organisms. Genealogical analyses of ciliate alpha-tubulin sequences reveal five apparently recent gene duplications. Comparisons of paralogs in different ciliates implicate differing patterns of substitutions (e.g., ratios of replacement/synonymous nucleotides and radical/conservative amino acids) following duplication. Most substitutions between paralogs in Euplotes crassus, Halteria grandinella and Paramecium tetraurelia are synonymous. In contrast, alpha-tubulin paralogs within Stylonychia lemnae and Chilodonella uncinata are evolving at significantly different rates and have higher ratios of both replacement substitutions to synonymous substitutions and radical amino acid changes to conservative amino acid changes. Moreover, the amino acid substitutions in C. uncinata and S. lemnae paralogs are limited to short stretches that correspond to functionally important regions of the alpha-tubulin protein. The topology of ciliate alpha-tubulin genealogies are inconsistent with taxonomy based on morphology and other molecular markers, which may be due to taxonomic sampling, gene conversion, unequal rates of evolution, or asymmetric patterns of gene duplication and loss.     

Cladistic biogeography and the art of discovery

Aims

Cladistic biogeography is about discovering geographical congruence. The agreement of several taxon‐area cladograms (TACs) rarely yields a perfect result. Areas may overlap, taxa may not be evenly distributed, and thus, ambiguity may be prevalent in the data. Ambiguity is incongruence and may be resolved by reducing paralogy and resolving potential information. Recently, several new approaches in cladistic biogeography [i.e. Brooks parsimony analysis (BPA), Assumption 0] interpret ambiguity as congruence. These methods are problematic, as they are generational. Methods constructed under the generation paradigm are flawed concepts that are immunized from falsifying evidence. A critique of modified BPA reveals that taking an evolutionary stance in biogeography leads to flaws in implementation.

Methods

Area cladistics is a new development in cladistic biogeography. Area cladistics adopts paralogy‐free subtree analysis using Assumption 2, to discover the relative positions of continents through time.

Results

Geographical congruence is the result of allopatric (geographical) speciation. Vicariance, dispersal and combinations of both, are recognized causes for allopatric speciation. Area cladistics highlights the concept that all these events occur in response to geological changes (e.g. continental drift) either directly, by geographical boundaries, or indirectly, at the level of ocean currents. Samples of chosen examples all respond to the geological process. The examples include Ordovician–Silurian and Lower Devonian trilobites to yield a general areagram which is a representational branching diagram that depicts the relationships of areas.

Main conclusion

Finding one common biogeographical pattern from several unrelated groups is a qualitative approach to interpret the positions of continental margins through time. Area cladistics is not a substitute for palaeomaps that are derived from palaeomagnetic data, but general areagrams adding to the body of knowledge that yields more precise interpretations of the earth's past.

     

Ten Years of Collaborative Progress in the Quest for Orthologs

Accurate determination of the evolutionary relationships between genes is a foundational challenge in biology. Homology—evolutionary relatedness—is in many cases readily determined based on sequence similarity analysis. By contrast, whether or not two genes directly descended from a common ancestor by a speciation event (orthologs) or duplication event (paralogs) is more challenging, yet provides critical information on the history of a gene. Since 2009, this task has been the focus of the Quest for Orthologs (QFO) Consortium. The sixth QFO meeting took place in Okazaki, Japan in conjunction with the 67th National Institute for Basic Biology conference. Here, we report recent advances, applications, and oncoming challenges that were discussed during the conference. Steady progress has been made toward standardization and scalability of new and existing tools. A feature of the conference was the presentation of a panel of accessible tools for phylogenetic profiling and several developments to bring orthology beyond the gene unit—from domains to networks. This meeting brought into light several challenges to come: leveraging orthology computations to get the most of the incoming avalanche of genomic data, integrating orthology from domain to biological network levels, building better gene models, and adapting orthology approaches to the broad evolutionary and genomic diversity recognized in different forms of life and viruses.     

Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal

Scorpions represent an iconic lineage of arthropods, historically renowned for their unique bauplan, ancient fossil record and venom potency. Yet, higher level relationships of scorpions, based exclusively on morphology, remain virtually untested, and no multilocus molecular phylogeny has been deployed heretofore towards assessing the basal tree topology. We applied a phylogenomic assessment to resolve scorpion phylogeny, for the first time, to our knowledge, sampling extensive molecular sequence data from all superfamilies and examining basal relationships with up to 5025 genes. Analyses of supermatrices as well as species tree approaches converged upon a robust basal topology of scorpions that is entirely at odds with traditional systematics and controverts previous understanding of scorpion evolutionary history. All analyses unanimously support a single origin of katoikogenic development, a form of parental investment wherein embryos are nurtured by direct connections to the parent''s digestive system. Based on the phylogeny obtained herein, we propose the following systematic emendations: Caraboctonidae is transferred to Chactoidea new superfamilial assignment; superfamily Bothriuroidea revalidated is resurrected and Bothriuridae transferred therein; and Chaerilida and Pseudochactida are synonymized with Buthida new parvordinal synonymies.     

Assumption 2: opaque to intuition?

Aim The aim of this paper was to revise the historical biogeographical method for resolving complicated distribution patterns through a technique that has come to be called assumption 2. Assumption 2 was used to resolve multiple areas on a single terminal branch (masts) as well as paralogous and missing areas in two or more areagrams. Recent examples, however, have shown that assumption 2 may be using rather than resolving paralogy. The paper attempts to resolve this problem by formulating a separate procedure to avoid using paralogous (redundant) area data in area cladistic analyses. Method The revision results in a new derivative method, the transparent method, to replace assumptions 1 and 2. It separates the procedures for resolving paralogy and for solving distribution patterns that occur in more than one area (masts). Results Several hypothetical examples show how the transparent method reduces paralogy and masts. The results show that paralogy can be reduced if the paralogy subtree method is applied after uncovering all possible relationships as single components on the terminals of areagrams. Conclusion The transparent method is a significant step forward in cladistic biogeography as it utilizes area relationships rather than generating general areagrams based on paralogous data.     

Haploid,diploid, and pooled exome capture recapitulate features of biology and paralogy in two non-model tree species

Despite their suitability for studying evolution, many conifer species have large and repetitive giga-genomes (16–31 Gbp) that create hurdles to producing high coverage SNP data sets that capture diversity from across the entirety of the genome. Due in part to multiple ancient whole genome duplication events, gene family expansion and subsequent evolution within Pinaceae, false diversity from the misalignment of paralog copies creates further challenges in accurately and reproducibly inferring evolutionary history from sequence data. Here, we leverage the cost-saving benefits of pool-seq and exome-capture to discover SNPs in two conifer species, Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco, Pinaceae) and jack pine (Pinus banksiana Lamb., Pinaceae). We show, using minimal baseline filtering, that allele frequencies estimated from pooled individuals show a strong, positive correlation with those estimated by sequencing the same population as individuals (r > .948), on par with such comparisons made in model organisms. Further, we highlight the utility of haploid megagametophyte tissue for identifying sites that are probably due to misaligned paralogs. Together with additional minor filtering, we show that it is possible to remove many of the loci with large frequency estimate discrepancies between individual and pooled sequencing approaches, improving the correlation further (r > .973). Our work addresses bioinformatic challenges in non-model organisms with large and complex genomes, highlights the use of megagametophyte tissue for the identification of paralogous artefacts, and suggests the combination of pool-seq and exome capture to be robust for further evolutionary hypothesis testing in these systems.     

Biogeography of Nicotiana section Suaveolentes (Solanaceae) reveals geographical tracks in arid Australia

Aim Nicotiana section Suaveolentes is largely endemic to Australia but includes one species endemic to Africa, one to New Caledonia and Tongatupa, and one to the Marquesas Islands in the Pacific. Other sections of Nicotiana are found in the New World. In Australia, Suaveolentes is widespread across the continent, with many taxa adapted to the Eremean zone. We aim to analyse the biogeography of the Australian clade, both to shed light on the evolution of the group and to determine general area relationships that provide insight into the history of the arid‐zone biota. Location Mesic and arid regions of continental Australia, the Central–South Pacific and Namibia, Africa. Methods A phylogeny of Suaveolentes, based on morphology and molecular data, was used to analyse the relationships of areas in which the taxa occur. The section is monophyletic, and all but three taxa were included (25). The method of paralogy‐free subtree analysis was employed, with the basal taxon Nicotiana africana used as the outgroup. Results Paralogy‐free subtree analysis found five area subtrees that, when combined, resulted in a minimal area cladogram with six resolved nodes. Pacific and mesic eastern Australia (including Lord Howe Island) are at the base of the area cladogram, followed by the differentiation of North West Australia and later South East Australia. Arid regions of Australia are related, revealing three biogeographical tracks: a northern track including the Great Sandy Desert and Tanami, which are related to the Pilbara; a central track relating the Western Desert, Central Ranges, Eastern Desert and North East Interzone; and a southern track relating the South West Interzone, Nullarbor, Adelaide/Eyre and the South East Interzone. Plesiomorphic taxa with chromosome number n = 24–23 occur on the periphery of the continent, and derived taxa with n = 21, 20, 18, 16–15 identify the tracks across arid Australia. Main conclusions The patterns of distribution and differentiation of Suaveolentes in Australia show that the age of the clade is at least Early Miocene, dating to before the onset of aridification in Australia about 15 Ma. The patterns are also interpreted as evidence that it was vicariance that largely shaped speciation in the Eremean zone, with range expansion of some widespread taxa probably occurring in the most recent cycles of severe drying and mobilization of desert dune sands.     

Phylogenetic relationships among arecoid palms (Arecaceae: Arecoideae)

Background and Aims

The Arecoideae is the largest and most diverse of the five subfamilies of palms (Arecaceae/Palmae), containing >50 % of the species in the family. Despite its importance, phylogenetic relationships among Arecoideae are poorly understood. Here the most densely sampled phylogenetic analysis of Arecoideae available to date is presented. The results are used to test the current classification of the subfamily and to identify priority areas for future research.

Methods

DNA sequence data for the low-copy nuclear genes PRK and RPB2 were collected from 190 palm species, covering 103 (96 %) genera of Arecoideae. The data were analysed using the parsimony ratchet, maximum likelihood, and both likelihood and parsimony bootstrapping.

Key Results and Conclusions

Despite the recovery of paralogues and pseudogenes in a small number of taxa, PRK and RPB2 were both highly informative, producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. Simultaneous analyses of the combined data sets provided additional resolution and support. Two areas of incongruence between PRK and RPB2 were strongly supported by the bootstrap relating to the placement of tribes Chamaedoreeae, Iriarteeae and Reinhardtieae; the causes of this incongruence remain uncertain. The current classification within Arecoideae was strongly supported by the present data. Of the 14 tribes and 14 sub-tribes in the classification, only five sub-tribes from tribe Areceae (Basseliniinae, Linospadicinae, Oncospermatinae, Rhopalostylidinae and Verschaffeltiinae) failed to receive support. Three major higher level clades were strongly supported: (1) the RRC clade (Roystoneeae, Reinhardtieae and Cocoseae), (2) the POS clade (Podococceae, Oranieae and Sclerospermeae) and (3) the core arecoid clade (Areceae, Euterpeae, Geonomateae, Leopoldinieae, Manicarieae and Pelagodoxeae). However, new data sources are required to elucidate ambiguities that remain in phylogenetic relationships among and within the major groups of Arecoideae, as well as within the Areceae, the largest tribe in the palm family.