scholarly journals Population genomics supports clonal reproduction and multiple gains and losses of parasitic abilities in the most devastating nematode plant pest

2018 ◽  
Author(s):  
Georgios D. Koutsovoulos ◽  
Eder Marques ◽  
Marie-Jeanne Arguel ◽  
Laurent Duret ◽  
Andressa C.Z. Machado ◽  
...  
Keyword(s):  
Population Genomics ◽  
Phylogenetic Signal ◽  
Clonal Reproduction ◽  
Small Scale ◽  
Biological Traits ◽  
Host Races ◽  
Genome Variability ◽  
Plant Pest ◽  
Ecological Success ◽  
Gains And Losses

ABSTRACTThe most devastating nematodes to worldwide agriculture are the root-knot nematodes with Meloidogyne incognita being the most widely distributed and damaging species. This parasitic and ecological success seem surprising given its supposed obligatory clonal reproduction. Clonal reproduction has been suspected based on cytological observations but, so far, never confirmed by population genomics data. At the species level, M. incognita is highly polyphagous with thousands of host plants. However, the host range varies among different M. incognita isolates that may present distinct and more restricted host compatibilities. Historically, four ‘host races’ had been defined as a function of ranges of compatible and incompatible plants. We sequenced the genomes of 11 isolates across Brazil, covering these four distinct races to assess (i) how clonal reproduction is and (ii) how the level of genome variability associates with biological traits such as the host races, affected agronomic culture, and geographical distribution. By aligning the genomic reads of the isolates to the M. incognita reference genome assembly, we identified SNV and small-scale insertions/deletions. Analysis of linkage disequilibrium and 4-gametes test, showed no sign of recombination, confirming the clonal mode of reproduction of M. incognita. We showed that there are relatively few point variations between the different isolates, and these variations show no significant association with either the host races, the geographical origin of the samples or the host plant on which they have been collected. Due to the lack of phylogenetic signal underlying their existence, we recommend the discontinuation of the terminology ‘race’. Overall, these results suggest that multiple gains and losses of parasitic abilities and adaptations to different environmental conditions account for the broad host spectrum and wide geographic distribution of M. incognita. Hence, this nematode constitutes a model species to study adaptability without sexual recombination and overall low genomic variations in animals.

scholarly journals Population genomics supports clonal reproduction and multiple independent gains and losses of parasitic abilities in the most devastating nematode pest

2019 ◽  
Vol 13 (2) ◽  
pp. 442-457 ◽  
Author(s):  
Georgios D. Koutsovoulos ◽  
Eder Marques ◽  
Marie‐Jeanne Arguel ◽  
Laurent Duret ◽  
Andressa C. Z. Machado ◽  
...  
Keyword(s):  
Population Genomics ◽  
Clonal Reproduction ◽  
Gains And Losses

scholarly journals Fishing for function: the use of biological traits to evaluate the effects of multispecies fisheries on the functioning of fisheries assemblages

2016 ◽  
Vol 73 (4) ◽  
pp. 1091-1103 ◽  
Author(s):  
Martha Koutsidi ◽  
Evangelos Tzanatos ◽  
Athanassios Machias ◽  
Vassiliki Vassilopoulou
Keyword(s):  
Functional Traits ◽  
Fisheries Management ◽  
Eastern Mediterranean ◽  
Ecosystem Approach ◽  
Purse Seine ◽  
Small Scale ◽  
Biological Traits ◽  
Multispecies Fisheries ◽  
Important Target ◽  
The Relationship

Abstract The Ecosystem Approach to Fisheries Management claims that fisheries management should take into account the ecosystem processes; in that context, it is useful to examine the functional traits of fisheries assemblages. This can be a challenge in multispecies fisheries. We used 21 biological traits of 86 species to investigate the relationship between-species and trait composition and to identify species with rare functional traits. Combining these traits with two catch datasets from the eastern Mediterranean (Patraikos Gulf: small-scale fleet, eastern Ionian Sea: entire multispecies fleet), we investigated whether certain fishing tactics or gears tend to remove specific traits, using multivariate methodologies. Species and traits composition of the catches were related, but an important part of trait variability was not explained by species composition. Rare traits and trait combinations were found for important target or bycatch species. Differences in the traits composition of fishing operations were revealed both between fishing tactics (Patraikos) as well as gears and areas (eastern Ionian); hierarchical clustering and MDS indicated the distinction of purse-seine catches at gear level. SIMPER analysis by trait indicated associations of certain trait categories mainly with purse-seines (at gear level) and longline métiers and a trammel-net métier (at métier level). The identification of rare traits or their combinations can have significant management implications as overfishing of the species with these traits could result in altering assemblage functioning. It seems that the multispecies character of the benthic fisheries results in a balanced trait removal, while management should regulate the effects of purse-seine fisheries on the fisheries assemblage functioning. Further investigation of the functions that fishing may remove from the ecosystem could contribute to understanding the effects of fishing and reveal overlooked aspects useful for the improvement of fisheries management.

scholarly journals Evolutionary patterns of range size, abundance and species richness in Amazonian trees

2016 ◽  
Author(s):  
Kyle Dexter ◽  
Jérôme Chave
Keyword(s):  
Species Richness ◽  
Phylogenetic Signal ◽  
Negative Relationship ◽  
Range Size ◽  
Biological Traits ◽  
Evolutionary Patterns ◽  
Phylogenetically Independent Contrasts ◽  
Significant Negative Relationship ◽  
The Mean ◽  
Amazonian Trees

Amazonian tree species vary enormously in their total abundance and range size, while Amazonian tree genera vary greatly in species richness. Here, we construct a phylogenetic hypothesis that represents half of Amazonian tree genera in order to analyse evolutionary patterns of range size, abundance, and species richness. We find several clear, broad-scale patterns. Firstly, there is significant phylogenetic signal for all three characteristics, i.e. closely related genera tend to have similar numbers of species and similar mean range size and abundance. Additionally, the species richness of genera shows a significant, negative relationship with the mean range size and abundance of their constituent species, while mean range size and abundance are significantly, positively correlated. These correlations are stronger in the raw data, but still significant when using phylogenetically independent contrasts. We suggest that tree stature and/or other phylogenetically related biological traits underlie these results. Lineages comprised of small-statured trees show greater species richness and smaller range sizes and abundances. Lastly, the phylogenetic signal that we evidence for range size suggests that should many small ranged species go extinct, greater phylogenetic diversity may be lost than expected if range size were distributed randomly across the phylogeny.

scholarly journals Phylogenetic signal in extinction selectivity in Devonian terebratulide brachiopods

Paleobiology ◽  
10.1666/14006 ◽  
2014 ◽  
Vol 40 (4) ◽  
pp. 675-692 ◽  
Author(s):  
Paul G. Harnik ◽  
Paul C. Fitzgerald ◽  
Jonathan L. Payne ◽  
Sandra J. Carlson
Keyword(s):  
Body Size ◽  
Fossil Record ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Positive Association ◽  
Range Size ◽  
Biological Traits ◽  
Significant Positive Association ◽  
Extinction Selectivity

Determining which biological traits affect taxonomic durations is critical for explaining macroevolutionary patterns. Two approaches are commonly used to investigate the associations between traits and durations and/or extinction and origination rates: analyses of taxonomic occurrence patterns in the fossil record and comparative phylogenetic analyses, predominantly of extant taxa. By capitalizing upon the empirical record of past extinctions, paleontological data avoid some of the limitations of existing methods for inferring extinction and origination rates from molecular phylogenies. However, most paleontological studies of extinction selectivity have ignored phylogenetic relationships because there is a dearth of phylogenetic hypotheses for diverse non-vertebrate higher taxa in the fossil record. This omission inflates the degrees of freedom in statistical analyses and leaves open the possibility that observed associations are indirect, reflecting shared evolutionary history rather than the direct influence of particular traits on durations. Here we investigate global patterns of extinction selectivity in Devonian terebratulide brachiopods and compare the results of taxonomic vs. phylogenetic approaches. Regression models that assume independence among taxa provide support for a positive association between geographic range size and genus duration but do not indicate an association between body size and genus duration. Brownian motion models of trait evolution identify significant similarities in body size, range size, and duration among closely related terebratulide genera. We use phylogenetic regression to account for shared evolutionary history and find support for a significant positive association between range size and duration among terebratulides that is also phylogenetically structured. The estimated range size–duration relationship is moderately weaker in the phylogenetic analysis due to the down-weighting of closely related genera that were both broadly distributed and long lived; however, this change in slope is not statistically significant. These results provide evidence for the phylogenetic conservatism of organismal and emergent traits, yet also the general phylogenetic independence of the relationship between range size and duration.

scholarly journals Phylogenetic non-independence in rates of trait evolution

2018 ◽  
Vol 14 (10) ◽  
pp. 20180502 ◽  
Author(s):  
Manabu Sakamoto ◽  
Chris Venditti
Keyword(s):  
Statistical Power ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Small Sample ◽  
Evolutionary Rates ◽  
Biological Traits ◽  
Beak Shape ◽  
Rates Of Evolution ◽  
Shared Ancestry ◽  
History Of

Statistical non-independence of species’ biological traits is recognized in most traits under selection. Yet, whether or not the evolutionary rates of such biological traits are statistically non-independent remains to be tested. Here, we test the hypothesis that phenotypic evolutionary rates are non-independent, i.e. contain phylogenetic signal, using empirical rates of evolution in three separate traits: body mass in mammals, beak shape in birds and bite force in amniotes. Specifically, we test if evolutionary rates are phylogenetically interdependent. We find evidence for phylogenetic signal in evolutionary rates in all three case studies. While phylogenetic signal diminishes deeper in time, this is reflective of statistical power owing to small sample and effect sizes. When effect size is large, e.g. owing to the presence of fossil tips, we detect high phylogenetic signals even in deeper time slices. Thus, we recommend that rates be treated as being non-independent throughout the evolutionary history of the group of organisms under study, and any summaries or analyses of rates through time—including associations of rates with traits—need to account for the undesired effects of shared ancestry.

scholarly journals Detecting Phylogenetic Signal and Adaptation in Papionin Cranial Shape by Decomposing Variation at Different Spatial Scales

2020 ◽  
Author(s):  
Nicole D S Grunstra ◽  
Silvester Bartsch ◽  
Anne Le Maître ◽  
Philipp Mitteroecker
Keyword(s):  
Large Scale ◽  
Phylogenetic Signal ◽  
Spatial Scales ◽  
Functional Adaptation ◽  
Small Scale ◽  
Phylogenetic Distance ◽  
Shape Features ◽  
Shape Variation ◽  
Outline Shape ◽  
Cranial Shape

Abstract Phylogenetic reconstruction based on morphometric data is hampered by homoplasies. For example, many similarities in cranial form between primate taxa more strongly reflect ecological similarities rather than phylogenetic relatedness. However, the way in which the different cranial bones constitute cranial form is, if at all, of less functional relevance and thus largely hidden from selection. We propose that these “constructional details” are better indicators of phylogenetic history than any large-scale shape feature or raw form variable. Within a geometric morphometric context, we show how to analyze the relative extent of bones independently of differences in overall shape. We also show how to decompose total shape variation into small-scale and large-scale shape variation. We apply both methods to the midsagittal cranial morphology of papionin monkeys, which are well known for the discrepancy between morphological similarities and phylogenetic relationships. We study phylogenetic signal and functional adaptation using a molecular phylogeny and contextual data on feeding ecology and locomotor behavior. As expected, total cranial shape, bone outline shape, and large-scale shape features were only weakly associated with phylogenetic distance. But the relative bone contributions and small-scale shape features were both highly correlated with phylogenetic distances. By contrast, the association with ecological and behavioral variables was strongest for the outline shape and large-scale shape features. Studies of morphological adaptation and phylogenetic history thus profit from a decomposition of shape variation into different spatial scales.

Recent Advances in Population Genomics of Plant-Parasitic Nematodes

2020 ◽  
pp. PHYTO-09-20-041
Author(s):  
Josselin Montarry ◽  
Benjamin Mimee ◽  
Etienne G. J. Danchin ◽  
Georgios D. Koutsovoulos ◽  
Dave T. Ste-Croix ◽  
...  
Keyword(s):  
Crop Production ◽  
High Throughput Sequencing ◽  
Population Genomics ◽  
Parasitic Nematodes ◽  
Agricultural Crop ◽  
Plant Parasitic Nematodes ◽  
Evolutionary Potential ◽  
Global Food Security ◽  
Genome Variability ◽  
Plant Parasitic

Plant-parasitic nematodes are a costly burden of crop production. Ubiquitous in nature, phytoparasitic nematodes are associated with nearly every important agricultural crop and represent a significant constraint on global food security. Population genetics is a key discipline in plant nematology to understand aspects of the life strategies of these parasites, in particular their modes of reproduction, geographic origins, evolutionary histories, and dispersion abilities. Advances in high-throughput sequencing technologies have enabled a recent but active effort in genomic analyses of plant-parasitic nematodes. Such genomic approaches applied to multiple populations are providing new insights into the molecular and evolutionary processes that underpin the establishment of these nematodes and into a better understanding of the genetic and mechanistic basis of their pathogenicity and adaptation to their host plants. In this review, we attempt to update information about genome resources and genotyping techniques useful for nematologists who are thinking about initiating population genomics or genome sequencing projects. This review is intended also to foster the development of population genomics in plant-parasitic nematodes through highlighting recent publications that illustrate the potential for this approach to identify novel molecular markers or genes of interest and improve our knowledge of the genome variability, pathogenicity, and evolutionary potential of plant-parasitic nematodes.

scholarly journals Evolutionary patterns of range size, abundance and species richness in Amazonian trees

2016 ◽  
Author(s):  
Kyle Dexter ◽  
Jérôme Chave
Keyword(s):  
Species Richness ◽  
Phylogenetic Signal ◽  
Negative Relationship ◽  
Range Size ◽  
Biological Traits ◽  
Evolutionary Patterns ◽  
Phylogenetically Independent Contrasts ◽  
Significant Negative Relationship ◽  
The Mean ◽  
Amazonian Trees

Amazonian tree species vary enormously in their total abundance and range size, while Amazonian tree genera vary greatly in species richness. Here, we construct a phylogenetic hypothesis that represents half of Amazonian tree genera in order to analyse evolutionary patterns of range size, abundance, and species richness. We find several clear, broad-scale patterns. Firstly, there is significant phylogenetic signal for all three characteristics, i.e. closely related genera tend to have similar numbers of species and similar mean range size and abundance. Additionally, the species richness of genera shows a significant, negative relationship with the mean range size and abundance of their constituent species, while mean range size and abundance are significantly, positively correlated. These correlations are stronger in the raw data, but still significant when using phylogenetically independent contrasts. We suggest that tree stature and/or other phylogenetically related biological traits underlie these results. Lineages comprised of small-statured trees show greater species richness and smaller range sizes and abundances. Lastly, the phylogenetic signal that we evidence for range size suggests that should many small ranged species go extinct, greater phylogenetic diversity may be lost than expected if range size were distributed randomly across the phylogeny.

A simple skeletal measurement effectively predicts climbing behaviour in a diverse clade of small mammals

2019 ◽  
Author(s):  
Jonathan A Nations ◽  
Lawrence R Heaney ◽  
Terrence C Demos ◽  
Anang S Achmadi ◽  
Kevin C Rowe ◽  
...  
Keyword(s):  
Small Mammals ◽  
Mixed Models ◽  
Phylogenetic Signal ◽  
Tail Length ◽  
Climbing Behaviour ◽  
Murine Rodents ◽  
Ecological Success ◽  
Best Fit ◽  
Digit Length ◽  
Skeletal Measurement

AbstractArboreal locomotion allows access to above-ground resources and might have fostered the diversification of mammals. Nevertheless, simple morphological measurements that consistently correlate with arboreality remain indefinable. As such, the climbing habits of many species of mammals, living and extinct, remain speculative. We collected quantitative data on the climbing tendencies of 20 species of murine rodents, an ecologically and morphologically diverse clade. We leveraged Bayesian phylogenetic mixed models (BPMMs), incorporating intraspecific variation and phylogenetic uncertainty, to determine which, if any, traits (17 skeletal indices) predict climbing frequency. We used ordinal BPMMs to test the ability of the indices to place 48 murine species that lack quantitative climbing data into three qualitative locomotor categories (terrestrial, general and arboreal). Only two indices (both measures of relative digit length) accurately predict locomotor styles, with manus digit length showing the best fit. Manus digit length has low phylogenetic signal, is largely explained by locomotor ecology and might effectively predict locomotion across a multitude of small mammals, including extinct species. Surprisingly, relative tail length, a common proxy for locomotion, was a poor predictor of climbing. In general, detailed, quantitative natural history data, such as those presented here, are needed to enhance our understanding of the evolutionary and ecological success of clades.

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