Phylogenetic Relationships Of Species Research Articles

Insights into comparative genomics, structural features, and phylogenetic relationship of species from Eurasian Aster and its related genera (Asteraceae: Astereae) based on complete chloroplast genome.

Aster L. is an economically and phylogenetically important genus in the tribe Astereae. Here, the complete plastomes of the eight Aster species were assembled and characterized using next-generation sequencing datasets. The results indicated the complete plastomes of Aster had a quadripartite structure. These genomes were 152,045-152,729 bp in length and contained 132-133 genes, including 87 protein-coding genes, 37-38 tRNA genes, and eight rRNA genes. Expansion or contraction of inverted repeat regions and forward, palindromic, complement, and reverse repeats were detected in the eight Aster species. Additionally, our analyses showed the richest type of simple sequence repeats was A/T mononucleotides, and 14 highly variable regions were discovered by analyzing the border regions, sequence divergence, and hotspots. Phylogenetic analyses indicated that 27 species in Astereae were clustered into six clades, i.e., A to D, North American, and outgroup clades, and supported that the genera Heteropappus, Kalimeris, and Heteroplexis are nested within Aster. The results indicated the clades B to D might be considered as genera. Divergence time estimate showed the clades A, B, C, and D diverged at 23.15 Mya, 15.13 Mya, 24.29 Mya, and 21.66 Mya, respectively. These results shed light on the phylogenetic relationships of Aster and provided new information on species identification of Aster and its related genera.

Weak phylogenetic effect on specialist plant assemblages and their persistence on habitat islands

AbstractAimThe influence of species phylogenetic relatedness on the formation of insular assemblages remains understudied in functional island biogeography, especially for terrestrial habitat islands (i.e. distinct habitat patches embedded in a matrix that differ in the prevailing environmental conditions). Here, we tested three eco‐evolutionary hypotheses: (1) functional specialization of species (i.e. specialism) is associated with phylogenetic clustering at the habitat archipelago scale, (2) such clustering increases with insularity at the habitat island scale and (3) traits indicative of effective local persistence strategies shape island specialism.LocationTerrestrial habitat islands, Europe (Fens in the Western Carpathians, Outcrops in Moravia and Mountaintops in the Cantabrian Range).TaxonAngiosperms.MethodsWe assessed the phylogenetic relatedness of habitat specialists in three different archipelagos composed of terrestrial habitat islands based on phylogenetic signals and phylogenetic diversity (PD) measures. We estimated the effect of insularity on PD using linear models and the effect of persistence traits on specialism using phylogenetic logistic regressions.ResultsOur hypotheses were largely not supported. Outcrop and mountaintop specialist assemblages did not exhibit any phylogenetic structuring, whereas fen specialists were clustered at the archipelago scale. Therefore, insularity seems not to act as a selective force for phylogenetic structure, and ecologically important persistence traits do not operate as precursors of specialism.Main ConclusionsOur results show that species phylogenetic relatedness plays a minor role in shaping habitat island specialist assemblages. Furthermore, the effects of phylogenetic relatedness on assemblages of island specialists are system and scale dependent. Finally, accounting for species' phylogenetic relatedness on persistence traits yielded results similar to previous studies, which corroborates the positive relationship between insularity and functional traits (indicative of enhanced plant persistence abilities with increasing within‐archipelago insularity).

The impact of species phylogenetic relatedness on invasion varies distinctly along resource versus non‐resource environmental gradients

Abstract Understanding why some, but not other, plant communities are vulnerable to alien invasive species is essential for predicting and managing biological invasions. Darwin proposed two seemingly contradictory hypotheses on how native‐invader relatedness influences invasion success, emphasizing, respectively, the importance of environmental filtering and competition between natives and invaders. Despite much recent empirical research on this topic, reconciling these two hypotheses, known as Darwin's naturalization conundrum, remains a challenge. Using plot‐level data from natural forests along elevational transects covering strong environmental gradients, we examined whether the invasion of the globally invasive species crofton weed (Ageratina adenophora) can be explained by environmental filtering and/or competition from closely related species linked to environmental gradients. Abundant precipitation, warm temperatures, open canopies and postfire environments facilitated A. adenophora invasion, whereas resident taxonomic richness suppressed its invasion. Importantly, we found that invader‐resident relatedness had a strong negative effect on invader cover under resource scarcity conditions (e.g. low water availability), but not under non‐resource environmental stress gradients (e.g. low temperature). Synthesis and applications. Our results suggest that the impact of species phylogenetic relatedness on invasion success varies distinctly along resource versus non‐resource environmental gradients. These results help to reconcile Darwin's naturalization conundrum, thereby improving the ability to predict the success of alien plant invasions in a changing world. Our study stresses the need to consider adjusting forest species composition to strengthen their resistance to invasion, while taking into account resource and non‐resource environmental gradients, particularly after wildfires.

Diversity of the genus Avrainvillea (Dichotomosiphonaceae, Chlorophyta): new insights and eight new species

ABSTRACT Avrainvillea is a green macroalgal genus of the family Dichotomosiphonaceae (order Bryopsidales). Many species have been morphologically described, but few studies have addressed the genetic diversity of this genus. Based on a rich collection of specimens from the tropical Western Atlantic, Indian and Pacific Oceans, we aimed to (1) reassess Avrainvillea species diversity through species delimitation analyses, (2) update their distribution ranges, (3) reconstruct the species phylogenetic relationships, based on a concatenated multilocus matrix (tufA, rbcL and 18S rDNA) and (4) revise their taxonomy and describe new species where necessary. Our species delimitation approach highlighted 23 secondary species hypotheses in our collection, including nine known and currently accepted species, four species complexes (A. amadelpha, A. lacerata, A. erecta-obscura and A. mazei-nigricans), and eight new species for which we provide descriptions: A. laciniata (Papua New Guinea), A. minima and A. pyrochroma (Madagascar), A. mollis and A. kanakiensis (New Caledonia), A. pavonina (Fiji), A. spongiosa (Pacific) and A. corticata (Indo-Pacific). We also propose the resurrection of A. gracillima Børgesen, the reinstatement of Avrainvillea lacerata var. robustior A.Gepp & E.S.Gepp, and the synonymy of A. rotumensis A.D.R.N’Yeurt, D.S.Littler & Littler with A. pacifica A.Gepp & E.S.Gepp. We complemented the taxonomic work by providing a contemporary dichotomous key for morphological identification of all extant species. Our multilocus phylogeny included 25 species of Dichotomosiphonaceae and recovered Avrainvillea as a polyphyletic group, divided into three distinct clades, with Cladocephalus luteofuscus positioned within the group. The species determined using the species delimitation approach were all monophyletic and 19 of them were highly supported. For the first time, this study also provided genetic sequences for A. asarifolia, A. clavatiramea, A. digitata, A. elliottii, A. fulva, A. gracillima, A. geppiorum, A. pacifica and A. obscura. HIGHLIGHTS • Avrainvillea is not monophyletic. • Reassessment of Avrainvillea species diversity delimited 23 secondary species hypotheses. • Eight new species of Avrainvillea were discovered in the Indo-Pacific.

Predator escape behaviour in threatened marsupials

AbstractEscaping from predators is fundamental for the survival of any prey species. Australian fauna within the ‘critical weight range’ (CWR; 35 g–5.5 kg) are vulnerable to introduced eutherian predators. The absence of co‐evolution between native marsupials and these novel predators may suggest that their antipredator behaviour towards the hunting strategies of these predators is inappropriate or ineffective. We quantified the escape behaviour of eight CWR marsupial taxa (three quadrupedal bandicoots and five bipedal macropods) to determine if differences in how they escape from predators indicate their ability to respond appropriately and effectively to introduced predators. Animals were filmed escaping through a runway and 20 measures relating to their gait, speed and path characteristics were recorded. These were reduced to four dimensions using multidimensional scaling (MDS): MDS1 linear speed versus agility, MDS2 acceleration style, MDS3 reactivity and MDS4 gait characteristics. We found a strong link between the phylogenetic relatedness of species and their use of linear speed or agility when fleeing (phylogenetic heritability, h2 = 0.96). Bipedal macropod species used straight‐line, fast escapes, which may be suited to escape pursuit predators. The quadrupedal bandicoots had an overall slower escape but were more likely to use sudden changes of direction, which can be successful if pursued by a larger, less mobile predator or where there is sufficient vegetation cover to obstruct pursuit. Repeated exposure increased linear speed (MDS1) and hastened the timing of acceleration (MDS2). The phylogenetic signal for escape speed/straightness suggests specific escape tactics may be constrained by morphology, although animals increased the intensity of their response after repeated exposure, suggesting training could enhance effective antipredator responses.

Population level genetic divergence and phylogenetic placement of Mexican shortfin mollies (Mollienesia: Poecilia: Poeciliidae)

Abstract Mexico is a megadiverse region with a complex geological history, but it remains unclear to what extent the distribution of freshwater fish has been influenced by geographic barriers. This study examines the population level genetic divergence and phylogenetic relationships of species in the shortfin group of the subgenus Mollienesia (genus Poecilia), a group of live-bearing fishes that are widely distributed across Mexico, with sampling at a small geographic scale. Samples from over 50 locations were analyzed for six species by using phylogenetic and haplotype network approaches to assess genetic diversity across geographic ranges and to refine the distributions of species in this group. The results indicate that Mexican species have diversified following multiple, independent invasions from Middle America. Two species found north of the Trans-Mexican Volcanic Belt (TMVB) and one transversal species exhibited weak phylogenetic structure, likely due to the lack of physiographic barriers, recent colonization, and high dispersal rates among regions. In contrast, three species found south of the TMVB exhibited strong phylogenetic structure, reflecting a longer presence in the area and multiple physiographic barriers that isolated populations. This study identified mechanisms driving divergence and speciation, expanded the known range of several species, and resolved taxonomic uncertainties of populations.

Molecular Structure and Phylogenetic Analyses of the Plastomes of Eight Sorbus Sensu Stricto Species.

Sorbus L. is a genus of controversy on its taxonomic concept due to great variations in morphological characteristics. Sorbus sensu stricto species, being monophyletic, are characterized as pinnate leaves. However, phylogenetic relationships of these species are somewhat fluid based on morphological characteristics and genetic markers. In this study, the chloroplast (cp) genomes of eight Sorbus s. str. species were characterized and compared with those of twelve released species in this genus. Our results indicated that the plastomes of the twenty Sorbus species had a conserved quadripartite structure, and 129 annotated genes had the same order and showed a good collinearity. Additionally, numerous SSRs were observed in the cp genome of each Sorbus species; most of the sequence variations appeared in non-coding regions, and four intergenic regions were identified as mutation spots. By contrast, protein-coding genes showed low variations under purifying selection. The phylogenetic and molecular-dating analysis showed that Sorbus was resolved into two major clades, in which S. americana forms one clade originating at 51.78 Ma, and the rest of Sorbus formed another clade, splitting at 36.77 Ma into two sister groups with high support values. These results provide a basis for further studying the phylogenetic relationship and biogeography of Sorbus species.

The spermatheca in the genus Dendroctonus (Curculionidae: Scolytinae): morphology, nomenclature, potential characters for taxonomic use and phylogenetic signal

In most members of the genus Dendroctonus, the usefulness of the spermatheca for taxonomic purposes has not been evaluated in depth; therefore, the aim of this study is to describe and compare the elements that integrate the female reproductive apparatus among Dendroctonus species, clarify their nomenclature and evaluate their interspecific variation to propose useful characteristics for their identification. In addition, we evaluated whether there is a structure between the shape of the receptacle and the phylogenetic relatedness of the species. The spermatheca consists of a sperm duct, a receptacle, and a gland; of these elements, the receptacle is the most taxonomically informative structure. The most closely related species of the D. frontalis complex show wide intraspecific variation in the shape and size of this structure, which precludes recognition of diagnostic features. However, there are differences among species groups in both shape and size in less closely related species such as D. approximatus, D. mexicanus, D. micans, D. parallelocollis and D. rhizophagus. A phylogenetic signal was detected in receptacle shape, and patterns of morphological similarity and phylogenetic relatedness of species were evident in the D. frontalis complex.

Niche conservatism and evolution of climatic tolerance in the Neotropical orchid genera Sobralia and Brasolia (Orchidaceae)

Sobralia and Brasolia form a large complex of Neotropical Orchidaceae. Although the molecular and morphological studies allowed to increase the rate of work on the modern classification of the taxa, they still require the attention as remaining without complete revision. The niche similarity analysis between representatives of Sobralia and recently segregated from this taxon—genus Brasolia is presented. The ecological tolerance evolution within the group was investigated with molecular clock analysis and phylogeny as the background. The phylogenetic analysis has confirmed the previous results and placed Brasolia representatives in a single clade with Elleanthus and Sobralia core as a separated group. The molecular clock analysis suggests that Sobralia and Brasolia are relatively young groups that evolved between 8.5 and 8 million years ago. Distribution of suitable niches of studied species is generally congruent with the known geographical ranges of particular taxa. The calculated niche overlap did not indicate any correlation between niche overlap and species phylogenetic relationships and remains low for both intra- and intergeneric relationships. The reconstruction of climatic tolerance evolution indicated that the studied species of Brasolia and Sobralia are characterized by generally similar ecological tolerance for most of the analyzed variables.

Nuclear ribosomal phylogeny of Brachystegia: new markers for new insights about rain forests and Miombo woodlands evolution

Background and aims – Brachystegia is a species-rich tree genus found in tropical Africa and a typical element of Miombo woodlands, a widely distributed subtype of the Zambezian savanna. Plastid DNA was shown to be largely uninformative to assess species phylogenetic relationships due to widespread chloroplast capture among species. Here, we aim to assess the capacity of nuclear ribosomal DNA (rDNA) to clarify the phylogeny of Brachystegia species while accounting for intra-individual site polymorphisms (2ISPs), which are often present in rDNA and potentially phylogenetically informative. Material and methods – Genome skimming sequencing on 47 samples representing 27 of the 29 currently recognized Brachystegia species, allowed us to retrieve complete nuclear ribosomal cistrons encoding for 18S, 5.8S, and 25S rRNA genes (35S rDNA). We reconstructed the Brachystegia phylogeny using Maximum Likelihood methods based on the standard substitution model or integrating 2ISPs (GENOTYPE implementation in RAxML-NG). We additionally tested the effect of partitioning the data (one partition for rDNA genes and one for the ITS1+ITS2). We also conducted network inferences (Neighbor-Net splits graph), as a strict bifurcative approach might not properly model topological uncertainty at shallow phylogenetic depth. Key results – 2ISPs-aware and standard phylogenetic reconstructions are largely congruent. We identified several well-supported main clades clarifying the species relationships, including two clades of Miombo woodlands species. Miombo Group A includes species with ovoid to globose axillary dormant buds, while Miombo Group B species have flattened ones. Two morphologically close Brachystegia species (B. kennedyi and B. leonensis) found in Guineo-Congolian rain forests form also a robustly supported clade. 2ISPs coding allowed to identify an additional Guineo-Congolian clade (B. eurycoma and B. nigerica). Ribosomal DNA therefore proves more useful to explore the generic phylogeny than plastid DNA but the species relationships within and among the main clades remain poorly resolved, probably due to recent diversification and/or recurrent hybridization, so that the diversification of Brachystegia remains to be more properly characterised. Conclusion – Nuclear and plastid phylogenetic reconstructions of Brachystegia species are discordant. Even if not well-resolved, rDNA phylograms and networks are characterized by taxonomic sorting, while we observe a strictly geographic sorting in the plastid dataset. Most of the species’ relationships remain to be characterized using additional nuclear markers combined with in-depth morphological investigations.

Phylogenetic Analysis Reveals Four New Species of Otidea from China.

Simple SummaryOtidea is a remarkable genus of ascomycetes. Members of the genus are diverse in ascomatal form, with split to entire, sessile to stipitate, cupulate to ear-shaped epigeous apothecia, as well as closed, solid ascomata in hypogeous taxa. They are distributed in the temperate to arctic-alpine regions of the northern hemisphere. China, located in the northern hemisphere, has a vast temperate zone, and a lot of new species of Otidea have been proposed recently. In this study, some specimens deposited in Chinese fungus herbaria and one newly collected Otidea specimen from northern China were studied using morphological and phylogenetic methods. The results indicate the presence of nine phylogenetic species of Otidea within the sample, four of them are described as new species, namely O. bomiensis, O. gongnaisiensis, O. hanzhongensis, and O. shennongjiana. Recognizing these new species will increase knowledge of species resources of Otidea in China.The emergence of molecular systematics has greatly helped researchers to identify fungal species. China has abundant Otidea species resources, and a number of new species of Otidea have been recently proposed. However, many old specimens in herbaria are mainly identified by morphology rather than molecular methods. In this study, 11 specimens deposited in Chinese herbaria and one newly collected Otidea species from northern China were identified based on morphological and phylogenetic analyses. Four gene fragments (ITS, LSU, rpb2, and tef1-α) were used to elucidate the phylogenetic relationships of species within Otidea. A total of nine phylogenetic species are recognized, of which four are described as new species, namely O. bomiensis, O. gongnaisiensis, O. hanzhongensis, and O. shennongjiana. Among the known species were O. aspera and O. sinensis.

Neckera, Forsstroemia and Alleniella (Neckeraceae, Bryophyta) redefined based on phylogenetic analyses

Phylogenetic relationships of species within the pleurocarpous moss genus Neckera s.l. (Neckeraceae) are reconstructed based on three genomic regions: the plastid rps4-trnT-trnL-trnF cluster and the rpl16 group II intron, as well as the internal transcribed spacer region of the nuclear ribosomal DNA (ITS1-5.8S-ITS2). The phylogenetic reconstruction suggests numerous taxonomic changes within the Neckeraceae. Two unispecific Asian genera are described as new: Taiwanobryopsis to accommodate Neckera warburgii, and Indoneckera to accommodate Neckera himalayana. Seven of the other “Neckera” species, all distributed in Asia, are transferred to Forsstroemia, and a further four Asian species to Taiwanobryum. Six Southern Hemisphere or tropical species (one from New Zealand, one from Africa, four from South America) are transferred to Alleniella. After these adjustments, Neckera becomes a northern hemisphere, mainly temperate, genus of c. 10 species that are absent from the tropics. It is in this context morphologically characterized by lack of paraphyllia (except N. californica) and an absent or weak costa. Alleniella has two species—the first diverging lineages—in the northern hemisphere, but the rest of the currently 15 species are distributed in the southern hemisphere and most of the species occur in mountain habitats in the tropics; it is however absent from tropical Asia and very scarce in Asia in general. Twelve of the 15 species have paraphyllia, which is the clearest morphological distinction from Neckera. Forsstroemia with 19 species, heavily concentrated in Asia, is the largest genus in the Neckeraceae. Clearly longer and more distinct costa distinguishes the genus from Neckera and Alleniella. Taiwanobryum is a morphologically heterogeneous Asian genus of nine species. Neckera decurrens Broth. is synonymized with Forsstroemia fauriei and Neckera valentiniana Besch. with Alleniella ehrenbergii.

A new obligate groundwater species of Asellus (Isopoda, Asellidae) from Iran

With only 43 described stygobionts and only two isopod species the obligate groundwater fauna of Iran, a vast country with over 10% of limestone surface, is inadequately known. Here, we report the discovery of Asellus ismailsezarii sp. nov. from Zagros mountains, the first eyeless and depigmented asellid isopod from Iran. The new species is morphologically similar to Asellus monticola Birstein, 1932, but it is eyeless and fully depigmented, has a slightly curved pereopod IV and does not bear any setae on proximal margins of exopodite of pleopods IV and V. Species phylogenetic relationships using original and datamined mitochondrial DNA and nuclear rDNA, and estimation of molecular divergences with other Asellus species, suggest that A. ismailsezarii sp. nov. is sister to a larger clade that also contains the European A. aquaticus species complex. Surface populations of Asellus have colonized groundwater at multiple occasions and localities, both in Europe and Asia, giving rise to species and subspecies that have evolved troglomorphisms, such as depigmentation and loss of eyes. Of the 37 formally described species and subspecies of Asellus, 15 are from groundwater, including A. ismailsezarii sp. nov. We predict that many more obligate groundwater Asellus taxa are yet to be discovered in Asia.

Restoring oak forests through direct seeding or planting: Protocol for a continental-scale experiment.

The choice of revegetating via direct seeding or planting nursery-grown seedlings influences the potential stresses suffered by seedlings such as herbivory and drought. The outcome of the balance between both revegetation methods may ultimately depend on how species identity and traits such as seed and seedling size interact with environmental conditions. To test this, we will conduct a continental-scale experiment consisting of one mini-experiment replicated by multiple participants across Europe. Each participant will establish a site with seeded and planted individuals of one or more native, locally growing oak (Quercus) species; the selection of this genus aims to favour continental-scale participation and to allow testing the response of a widely distributed genus of broad ecological and economic relevance. At each site, participants will follow the present protocol for seed collection, seeding in the field, nursery cultivation, outplanting, protection against herbivores, site maintenance, and measurement of seedling performance and environmental variables. Each measurement on each species at each site will produce one effect size; the data will be analysed through mixed-effects meta-analysis. With this approach we will assess the main effect of revegetation method, species, plant functional traits, and the potential effect of site-specific effect moderators. Overall, we will provide a continental-scale estimate on the seeding vs. planting dilemma and analyse to what extent the differences in environmental conditions across sites, seed size, functional traits, and the phylogenetic relatedness of species can account for the differences in the effect of revegetation method on seedling performance across study sites and species.

СИСТЕМАТИЧЕСКИЙ АНАЛИЗ ВИДОВ РОДА QUERCUS L. В ДЕНДРОЛОГИЧЕСКОМ ГЕРБАРИИ ВУЗА

The results of the analysis of Quercus L. species stored in the herbarium of the Department of Botany and Plant Physiology of Federal State Budget Educational Institution of Higher Education VSUFT (Voronezh) are presented. This herbarium of historical plant collections of the genus Quercus L. is critical for tracking changes in the genus, including the introduction and distribution of species. We examined the belonging of the species to systematic units – subgenus, section, subsection, row, using the traditional classification and the updated intrageneric classification of oaks. Information about the life form, plant height, date and place of collection of the specimen was recorded. We entered information into the database, which will further simplify the work on registration, revision of the herbarium fund and when replenishing herbarium specimens. Conclusions were drawn based on the results of the workabout changes in the taxonomic nature and phylogenetic relationships of species in Quercus L. genus

Molecular Phylogeny of Trifolium L. Section Trifolium with Reference to Chromosome Number and Subsections Delimitation.

The genus Trifolium is one of the largest genera of the legume family Fabaceae with ca. 255 species. The genus is divided into eight sections; the section Trifolium is a major section of the genus, comprising 73 species mainly distributed in the Mediterranean region. We used nuclear ribosomal DNA internal transcribed spacer (ITS) and morphological variation to reconsider the delimitation and phylogenetic relationships of species in the section Trifolium with reference to chromosomal variations. Bayesian analysis of ITS data delimited the species as three clades based on the analysis of ITS sequence and informative indels in combination with morphological variation. The phylogeny of the species by different analyses methods does not support their current delimitation in 17 subsections. The basic chromosome number x = 8 is the number for the genus Trifolium, from which x = 7, 6 and 5 were derived through successive aneuploidy events. With reference to the distribution of these numbers in the species of the section Trifolium, species in clade III and clade II are more evolved than species in clade I.

Songs in the genus Uromenus (Orthoptera: Tettigoniidae: Ephippigerini): A review with new information about some species.

With nearly 60 described forms Uromenus is the most species-rich genus of the tribe Ephippigerini, a west Palearctic group of flightless bush-crickets (katydids). As it is typical for bush-crickets, Uromenus males produce species-specific calling songs to attract females prepared to mate. These insects are relatively large and their songs have always components audible to humans. Nevertheless, acoustical information are available only for few species. Also the phylogenetic relationships of species and species groups are poorly known. In this paper we present new data on the song and morphology of several species (U. dyrrhachiacus, U. elegans, U. finoti, U. galvagnii, U. robustus, U. tobboganensis and U. innocentii) and give a review of all published acoustical data. Judging from the still few data, as in other Ephippigerini the song patterns often seem to contain species-group characteristics making them candidates to be used in phylogenetic studies. Additionally, we have studied the female stridulatory organs which are unique in structure in Ephippigerini and completely different from those of the males. Despite in Uromenus used only for defensive stridulation, possibly species-specific similarities in structure between males and females exist.

Methodological advances for hypothesis-driven ethnobiology.

Ethnobiology as a discipline has evolved increasingly to embrace theory-inspired and hypothesis-driven approaches to study why and how local people choose plants and animals they interact with and use for their livelihood. However, testing complex hypotheses or a network of ethnobiological hypotheses is challenging, particularly for data sets with non-independent observations due to species phylogenetic relatedness or socio-relational links between participants. Further, to account fully for the dynamics of local ecological knowledge, it is important to include the spatially explicit distribution of knowledge, changes in knowledge, and knowledge transmission and use. To promote the use of advanced statistical modelling approaches that address these limitations, we synthesize methodological advances for hypothesis-driven research in ethnobiology while highlighting the need for more figures than tables and more tables than text in ethnobiological literature. We present the ethnobiological motivations for conducting generalized linear mixed-effect modelling, structural equation modelling, phylogenetic generalized least squares, social network analysis, species distribution modelling, and predictive modelling. For each element of the proposed ethnobiologists quantitative toolbox, we present practical applications along with scripts for a widespread implementation. Because these statistical modelling approaches are rarely taught in most ethnobiological programs but are essential for careers in academia or industry, it is critical to promote workshops and short courses focused on these advanced methods. By embracing these quantitative modelling techniques without sacrificing qualitative approaches which provide essential context, ethnobiology will progress further towards an expansive interaction with other disciplines.

The use of taxonomic relationships among species in applied ecological research: Baseline, steps forward and future challenges

AbstractTaxonomy is more than a mere exercise of nomenclature and classification of biological diversity: it profiles the identity of species by investigating their biological and ecological traits. Taxonomy is intimately related to ecology which, in turn, cannot be a mere exercise in describing ecological patterns, but instead requires deep knowledge of species’ biological structures, roles, interactions and functions. Thus, the study of taxonomic and phylogenetic relatedness of species is of paramount importance in ecological research, enabling insights into potential evolutionary patterns and processes, allowing a more comprehensive view of biodiversity, and providing opportunities to improve the assessment and monitoring of ecological changes in time and space. The work of K. Robert (‘Bob’) Clarke forged new pathways in this direction, providing new ideas and statistical tools to include and exploit taxonomic relationships in applied marine ecological studies and beyond, also inspiring the next generation of ecologists. In this short review, we synthesise the application and development of these tools and concepts in marine biodiversity research over the last three decades and suggest future pathways in this evolving field.

Molecular phylogenetic relationships of Metastrongylus nematodes with emphasis on specimens from domestic pigs in Vietnam.

Lungworms of the genus Metastrongylus are parasitic nematodes in the respiratory tract of swine. Although they infect both wild boars and domestic pigs, studies on Metastrongylus infections in wild boars in Europe, the Americas and Africa are numerous, while those in domestic pigs are few. There are several studies analysing the molecular phylogenetic relationships of few individual Metastrongylus species with other nematode taxa, but there are no studies on the phylogenetic relationships of species within the genus Metastrongylus. In Southeast Asia, reports on swine lungworms are extremely scarce and do not include any nucleotide sequence data. Therefore, the aim of the present study is to survey Metastrongylus infection in domestic pigs raised in Dien Bien Province, Northern Vietnam, and to analyse the molecular phylogenetic relationships of Metastrongylus species. Based on morphological and molecular data, we identified two species: Metastrongylus apri and Metastrongylus pudendotectus. The prevalence of the former species was found to be significantly higher than the latter one (24.1% vs. 2.3%). We observed pigs exhibiting a coinfection with the two lungworm species or a single infection with only M. apri. However, we did not observe any pigs being infected with just M. pudendotectus. Vietnamese Metastrongylus specimens showed slight morphological and molecular differences compared to those from other countries. The molecular analyses revealed a close genetic relationship between M. apri and Metastrongylus salmi, while both these species were far distant from M. pudendotectus. The present study highlights the needs for further studies to clarify the morphological features and ecological and phylogenetic relationships of Metastrongylus species at the global scale.