scholarly journals Relationships between taxonomic and functional diversity: insights into assembly processes

Author(s):  
Doriane Stagnol ◽  
Lise Bacouillard ◽  
Dominique Davoult

Among the potential indicators of biodiversity, those based on the functional traits of species are interesting because they measure the aspects of diversity that potentially affect community assembly and function. However, trait-based approaches are still rarely considered and little is known about the degree to which taxonomic diversity (TD) and functional diversity (FD) are correlated. Yet, this relationship is thought to depend on the extent of ecological redundancy within the assemblage, i.e. the number of taxonomically distinct species that exhibit similar ecological functions. In this study, we characterized taxonomic and functional diversity within and between two marine habitats (rocky shore vs mudflats) under human-induced disturbances. Models were also used to test whether the relationship between TD and FD differed according to the indices used to characterize them. We found little effect of human disturbance on the shape of the TD-FD relationship, whereas communities of the mudflat appeared to be less redundant than those of rocky shore. This could be explained by the assembly rules of ecosystems: biotic filtering (competition and resource partitioning) reduces redundancy by selecting for functionally dissimilar species, whereas abiotic filtering increases redundancy by selecting for similar species sharing adaptations to a particular environment. The rocky shore environment is characterized by heterogeneity that allows the formation of distinct ecological niches that can be colonized by similar species: the abiotic filtering does not limit the redundancy permitted by habitat. Conversely, in the more homogeneous environment of mudflat, the biotic filter mitigates redundancy. Trait-mediated abiotic filtering appears to play an important role in community assembly in complex habitats, whereas the relative importance of competitive exclusion appears to be greater in homogeneous habitats.

Author(s):  
Doriane Stagnol ◽  
Lise Bacouillard ◽  
Dominique Davoult

Among the potential indicators of biodiversity, those based on the functional traits of species are interesting because they measure the aspects of diversity that potentially affect community assembly and function. However, trait-based approaches are still rarely considered and little is known about the degree to which taxonomic diversity (TD) and functional diversity (FD) are correlated. Yet, this relationship is thought to depend on the extent of ecological redundancy within the assemblage, i.e. the number of taxonomically distinct species that exhibit similar ecological functions. In this study, we characterized taxonomic and functional diversity within and between two marine habitats (rocky shore vs mudflats) under human-induced disturbances. Models were also used to test whether the relationship between TD and FD differed according to the indices used to characterize them. We found little effect of human disturbance on the shape of the TD-FD relationship, whereas communities of the mudflat appeared to be less redundant than those of rocky shore. This could be explained by the assembly rules of ecosystems: biotic filtering (competition and resource partitioning) reduces redundancy by selecting for functionally dissimilar species, whereas abiotic filtering increases redundancy by selecting for similar species sharing adaptations to a particular environment. The rocky shore environment is characterized by heterogeneity that allows the formation of distinct ecological niches that can be colonized by similar species: the abiotic filtering does not limit the redundancy permitted by habitat. Conversely, in the more homogeneous environment of mudflat, the biotic filter mitigates redundancy. Trait-mediated abiotic filtering appears to play an important role in community assembly in complex habitats, whereas the relative importance of competitive exclusion appears to be greater in homogeneous habitats.


2020 ◽  
Vol 16 (2) ◽  
pp. 20190738
Author(s):  
Benjamin M. Titus ◽  
Robert Laroche ◽  
Estefanía Rodríguez ◽  
Herman Wirshing ◽  
Christopher P. Meyer

All eukaryotic life engages in symbioses with a diverse community of bacteria that are essential for performing basic life functions. In many cases, eukaryotic organisms form additional symbioses with other macroscopic eukaryotes. The tightly linked physical interactions that characterize many macroscopic symbioses create opportunities for microbial transfer, which likely affects the diversity and function of individual microbiomes, and may ultimately lead to microbiome convergence between distantly related taxa. Here, we sequence the microbiomes of five species of clownfish-hosting sea anemones that co-occur on coral reefs in the Maldives. We test the importance of evolutionary history, clownfish symbiont association, and habitat on the taxonomic and predicted functional diversity of the microbiome, and explore signals of microbiome convergence in anemone taxa that have evolved symbioses with clownfishes independently. Our data indicate that host identity and clownfish association shapes the majority of the taxonomic diversity of the clownfish-hosting sea anemone microbiome, and predicted functional microbial diversity analyses demonstrate a convergence among host anemone microbiomes, which reflect increased functional diversity over individuals that do not host clownfishes. Further, we identify upregulated predicted microbial functions that are likely affected by clownfish presence. Taken together our study potentially reveals an even deeper metabolic coupling between clownfishes and their host anemones, and what could be a previously unknown mutualistic benefit to anemones that are symbiotic with clownfishes.


MycoKeys ◽  
2019 ◽  
Vol 50 ◽  
pp. 1-77 ◽  
Author(s):  
Sten Svantesson ◽  
Karl-Henrik Larsson ◽  
Urmas Kõljalg ◽  
Tom W. May ◽  
Patrik Cangren ◽  
...  

P.tristisis an ectomycorrhizal, corticioid fungus whose name is frequently assigned to collections of basidiomata as well as root tip and soil samples from a wide range of habitats and hosts across the northern hemisphere. Despite this, its identity is unclear; eight heterotypic taxa have in major reviews of the species been considered synonymous with or morphologically similar toP.tristis, but no sequence data from type specimens have been available.With the aim to clarify the taxonomy, systematics, morphology, ecology and geographical distribution ofP.tristisand its morphologically similar species, we studied their type specimens as well as 147 basidiomata collections of mostly North European material.We used gene trees generated in BEAST 2 and PhyML and species trees estimated in STACEY and ASTRAL to delimit species based on the ITS, LSU, Tef1α and mtSSU regions. We enriched our sampling with environmental ITS sequences from the UNITE database.We found theP.tristisgroup to contain 13 molecularly and morphologically distinct species. Three of these,P.tristis,P.umbrinaandP.atrofusca, are already known to science, while ten species are here described as new:P.sciastrasp. nov.,P.tristoidessp. nov.,P.umbrinascenssp. nov.,P.pinophilasp. nov.,P.alnophilasp. nov.,P.alobatasp. nov.,P.plurilobasp. nov.,P.abundilobasp. nov.,P.rotundisporasp. nov.andP.mediasp. nov.We discoveredP.rhizopunctataandP.atrofuscato form a sister clade to all other species inP.tristiss.l. These two species, unlike all other species in theP.tristiscomplex, are dimitic.In this study, we designate epitypes forP.tristis,P.umbrinaandHypochnopsisfuscataand lectotypes forAuriculariaphylacterisandThelephorabiennis. We show that the holotype ofHypochnussitnensisand the lectotype ofHypochnopsisfuscataare conspecific withP.tristis, but in the absence of molecular information we regardPseudotomentellalongisterigmataandHypochnusrhacodiumas doubtful taxa due to their aberrant morphology. We confirmA.phylacteris,TomentellabiennisandSeptobasidiumarachnoideumas excluded taxa, since their morphology clearly show that they belong to other genera. A key to the species of theP.tristisgroup is provided.We foundP.umbrinato be a common species with a wide, Holarctic distribution, forming ectomycorrhiza with a large number of host species in habitats ranging from tropical forests to the Arctic tundra. The other species in theP.tristisgroup were found to be less common and have narrower ecological niches.


2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Tamara N. Romanuk ◽  
Amrei Binzer ◽  
Nicolas Loeuille ◽  
W. Mather A. Carscallen ◽  
Neo D. Martinez

AbstractWhile natural communities are assembled by both ecological and evolutionary processes, ecological assembly processes have been studied much more and are rarely compared with evolutionary assembly processes. We address these disparities here by comparing community food webs assembled by simulating introductions of species from regional pools of species and from speciation events. Compared to introductions of trophically dissimilar species assumed to be more typical of invasions, introducing species trophically similar to native species assumed to be more typical of sympatric or parapatric speciation events caused fewer extinctions and assembled more empirically realistic networks by introducing more persistent species with higher trophic generality, vulnerability, and enduring similarity to native species. Such events also increased niche overlap and the persistence of both native and introduced species. Contrary to much competition theory, these findings suggest that evolutionary and other processes that more tightly pack ecological niches contribute more to ecosystem structure and function than previously thought.


Forests ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1159 ◽  
Author(s):  
Jinshi Xu ◽  
Han Dang ◽  
Mao Wang ◽  
Yongfu Chai ◽  
Yaoxin Guo ◽  
...  

Phylogenetic and functional diversities and their relationship are important for understanding community assembly, which relates to forest sustainability. Thus, both diversities have been used in ecological studies evaluating community responses to environmental changes. However, it is unclear whether these diversity measures can uncover the actual community assembly processes. Herein, we examined their utility to assess such assembly processes by analyzing similarities in phylogenetic, functional, and taxonomic α- and β-diversities along an elevational gradient. Additionally, we examined the relationships among environment, phylogeny, and functional traits within the community. Based on our results, we evaluated whether phylogenetic or functional diversity could better reveal the actual community assembly processes. We found that taxonomic, phylogenetic, and functional α-diversities were correlated with one another. Although the functional α-diversity showed a linear correlation with the elevational gradient, taxonomic and phylogenetic α-diversities showed unimodal patterns. Both phylogenetic and functional β-diversities correlated with taxonomic β-diversity, but there was no significant relationship between the former. Overall, our results evidenced that phylogenetic diversity and taxonomic diversity showed similar patterns, whereas functional diversity showed a relatively independent pattern, which may be due to limitations in the functional trait dimensions used in the present study. Although it is difficult to unravel whether the environment shapes phylogeny or functional traits within a community, phylogenetic diversity is a good proxy for assessing the assembly processes, whereas functional diversity may improve knowledge on the community by maximizing information about the functional trait dimensions.


Phytotaxa ◽  
2017 ◽  
Vol 295 (1) ◽  
pp. 49
Author(s):  
ALUWANI A. TSHIILA ◽  
SAMSON B.M. CHIMPHANGO ◽  
JAN-ADRIAAN VILJOEN ◽  
A. MUTHAMA MUASYA

Unclear boundaries between species hinder identification in the field and in herbaria, especially in species groups that can only be distinguished on the basis of subtle morphological and ecological features. One such taxon is Ficinia indica, widespread in the Greater Cape Floristic Region, growing on deep sandy soils between sea level and 1000 m elevation. Within its range, several phylogenetically related and morphologically similar species co-occur or occupy distinct habitats. Studies in herbaria show species in the Ficinia indica complex to be largely misidentified based on the use of qualitative information. Here, we investigate whether the six taxa recognized, based on one or a few characters, are supported as distinct species based on multivariate analysis of macro-morphological data. Two of the taxa were mostly separated whereas the other four taxa overlapped in multivariate space, but all the taxa could be distinguished using a single or a combination of morphological and ecological characters. We uphold the four previously recognized taxa (Ficinia argyropus, F. elatior, F. indica, F. laevis) as species, describe two new species (F. arnoldii and F. montana), and provide a dichotomous key for their identification.


Phytotaxa ◽  
2015 ◽  
Vol 205 (2) ◽  
pp. 90 ◽  
Author(s):  
XIN-LEI FAN ◽  
KEVIN D. HYDE ◽  
JIAN-KUI LIU ◽  
YING-MEI LIANG ◽  
CHENG-MING TIAN

The family Botryosphaeriaceae encompasses important plant-associated pathogens, endophytes and saprobes with a wide geographical and host distribution. Two dark-spored botryosphaeriaceous taxa associated with Rhus typhina dieback and canker disease were collected from Ningxia Province, in northwestern China. Morphology and multigene analysis (ITS, LSU and EF-1α) clearly distinguished this clade as a distinct species in the genus. Phaeobotryon rhois is introduced and illustrated as a new species in this paper. The species is characterized by its globose, unilocular fruiting bodies and small, brown, 1-septate conidia. It can be distinguished from the similar species P. cercidis, P. cupressi, P. mamane and P. quercicola based on host association and conidial size and colour.


2017 ◽  
Author(s):  
Arnaud Meng ◽  
Camille Marchet ◽  
Erwan Corre ◽  
Pierre Peterlongo ◽  
Adriana Alberti ◽  
...  

AbstractBackgroundStudy of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. The study of holobiont transcriptomes shares similarities with meta-transcriptomic, and hence, is also affected by challenges invoked above. Here we propose an innovative approach to tackle such difficulties which was applied to the study of marine holobiont models as a proof of concept.ResultsWe considered three holobionts models, of which two transcriptomes were previously assembled and published, and a yet unpublished transcriptome, to analyze their raw reads and assign them to the host and/or to the symbiont(s) using Short Read Connector, a k-mer based similarity method. We were able to define four distinct categories of reads for each holobiont transcriptome: host reads, symbiont reads, shared reads and unassigned reads. The result of the independent assemblies for each category within a transcriptome led to a significant diminution of de novo assembled chimeras compared to classical assembly methods. Combining independent functional and taxonomic annotations of each partner’s transcriptome is particularly convenient to explore the functional diversity of an holobiont. Finally, our strategy allowed to propose new functional annotations for two well-studied holobionts and a first transcriptome from a planktonic Radiolaria-Dinophyta system forming widespread symbiotic association for which our knowledge is limited. ConclusionsIn contrast to classical assembly approaches, our bioinformatic strategy not only allows biologists to studying separately host and symbiont data from a holobiont mixture, but also generates improved transcriptome assemblies. The use of Short Read Connector has proven to be an effective way to tackle meta-transcriptomic challenges to study holobiont systems composed of either well-studied or poorly characterized symbiotic lineages such as the newly sequenced marine plankton Radiolaria-Dinophyta symbiosis and ultimately expand our knowledge about these marine symbiotic associations.


Sociobiology ◽  
2016 ◽  
Vol 63 (3) ◽  
pp. 941 ◽  
Author(s):  
Luana Priscila de Carvalho Pereira ◽  
Fábio Souto Almeida ◽  
André Barbosa Vargas ◽  
Marcel Santos de Araújo ◽  
Antônio José Mayhé-Nunes ◽  
...  

The present study aimed at assessing the effects of climate seasonality on poneromorph ants in the Brazilian Amazon, by studying variations in composition, richness, and taxonomic and functional diversity. The study was carried out in the Tapirapé-Aquiri National Forest, southeastern Pará State. We collected poneromorph ants in three areas of native forest with pitfall traps and sardine baits on the ground and vegetation, in two dry and rainy seasons. We collected 46 species of poneromorph ants, which belong to two subfamilies and eleven genera. The species composition, richness and taxonomic diversity did not vary significantly between seasons. There was no significant difference in the frequency of species of functional groups between dry and rainy seasons. There was no significant difference in the average richness and average diversity of functional groups between the dry and rainy seasons. In our study we found no seasonal differences in composition, taxonomic and functional richness and diversity of poneromorph ants in the Amazon, which is useful for future studies that aim at using those ants as bioindicators. In addition, the identification of the species made in the present study has special relevance as it contributes to advance the knowledge of poneromorph ant diversity in the Amazon.


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