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Phylogeny and climate explain contrasting hydraulic traits in different life forms of 150 woody Fabaceae species

<ol> <li>The contrasting hydraulic traits observed among different plant life forms are shaped by entangled environmental and evolutionary processes. However, we lack an understanding of the relative importance of life form, climate and phylogeny in explaining the variance of hydraulic traits.</li> <li>We analyzed seven hydraulic traits and eleven climatic variables of 150 Fabaceae species representing three life forms from 62 sites worldwide, using phylogenetic comparative analyses and variance partitioning.</li> <li>The phylogenetic signal found in most traits disappeared after considering life form, indicating that phylogenetic conservatism in traits originated from the divergence among life forms. The trait-climate relationships were also phylogenetically dependent, implying that trait responses are driven by climate and phylogeny together. Variance partitioning showed that phylogeny and climate explained greater trait variation than life form did.</li> <li> Synthesis. The climate-driven hydraulic trait responses in Fabaceae still existed with phylogeny being considered, suggesting that this large family may be particularly sensitive to climate change. Our results emphasize the need to include phylogeny in plant hydraulic adaptation studies under future climate change.</li> </ol>

opencc-by-nc-4.0Jan 2024View details →

Figures 5-9 in A phylogeny of Carrerapyrgota Aczél (Diptera, Pyrgotidae)

Figures 5-9. Wings: Leptopyrgota sahlbergiana Frey (5); Stenopyrgota crassitibia Aczél (6); Idiopyrgota setiventris Aczél (7); Carrerapyrgota personata (Lutz & Lima) (8); C. miliaria Aczél (9). Scales: Fig. 5: 2 mm; Figs. 6-9: 1 mm. Fig. 6 modified from Mello & Lamas (2014), Fig. 7 modified from Mello & Lamas (2008), Figs. 8-9 modified from Mello et al. (2010).

Foliar endophyte diversity in eastern Asia-eastern North America disjunct tree species – Influences of host identity, environment, phylogeny, and geographic isolation

The well-known eastern Asia (EA) and eastern North America (ENA) floristic disjunction provides a unique system for biogeographic and evolutionary studies. Despite considerable interest in the disjunction, few studies have investigated the patterns and their underlying drivers of allopatric divergence in sister species or clades isolated in the two areas. Endophyte diversity and assembly in disjunct sister taxa, as an ecological trait, may have played an important role in the processes of allopatric evolution, but no studies have examined endophytes in these disjunct lineages. In this study, we compared foliar endophytes (including both fungi and bacteria) in 17 EA-ENA disjunct species pairs from genera representing conifers and major clades of angiosperms, as well as 23 species of Cornus from the US and China. We sequenced the ITS of fungi and 16S rDNA of bacteria to understand the composition of the endophyte community and gain insights into the relative roles of geographic isolation, host identity, phylogeny, and environment in shaping endophytic diversity patterns. We detected a much richer fungal than bacterial community in leaves of all species. Beta diversity varied greatly among individuals within species, between species, among genera, and among three natural environmental conditions. Based on a principal coordinates analysis, we found no close clustering of endophyte communities in samples from the same host plant species, from the same genus, or from the same geographic origin (i.e. EA or ENA) (when plants were grown in the same common garden), but we did detect clustering of samples from plants grown in the same environment (i.e., same geographic location). We observed separation of microbes in plant samples of the same species grown in different locations/environments. However, pooled samples across all species from the common garden with the same geographic origin (EA vs. ENA) showed a moderate level of dissimilarity in fungal endophytes between EA and ENA. An overall significant correlation between endophyte community dissimilarity and phylogenetic distance was detected among the disjunct genera but not among species of Cornus. However, significant correlation between order, family, and genera of endophytes and phylogenetic distance of Cornus species was observed. We also found no significant differences in Foliar Endophytic Fungal (FEF) communities between counterparts of disjunct species pairs in EA and ENA in most genera except in Liriodendron and Cornus, although the beta diversity within genera is high. Our results suggest important roles of host identity and environment (geographic locations), and a likely minor role of phylogenetic divergence and biogeographic isolation in shaping the pattern of foliar endophyte diversity and assembly in the EA-ENA disjunct genera, as well as in Cornus. The results further suggest that the sister taxa in EA and ENA are likely different in their foliar endophyte composition when growing in their native habitats due to differences in geographic locations and local environments, which is potentially a factor driving allopatric divergence of species functional features. This hypothesis can be tested by analysis of samples from native habitats.

Fossil calibrated molecular phylogenies of Southern cave weta

Aim: The biota of continents and islands are commonly considered to have a source-sink relationship, but small islands can harbour distinctive taxa. The distribution of four monotypic genera within the southern subfamily Macropathinae on young oceanic islands indicates a role for long-distance dispersal and extinction. We used molecular dating to estimate the timing of the southern radiation and infer potential processes involved. Location: Subantarctic islands, South Africa, South America, Australia, Aotearoa/New Zealand. Taxon: Southern hemisphere camel crickets subfamily Macropathinae within the Orthopteran family Rhaphidophoridae (Cave crickets/camel crickets/cave weta/tokoriro). Methods: Phylogenetic relationships were inferred from whole mtDNA genomes and nuclear sequences (45S cassette; four histones). We used a fossil and one palaeogeographic event to calibrate a molecular clock analysis. Results: We confirm that neither the Australian nor Aotearoa/New Zealand Rhaphidophoridae fauna are monophyletic. The Macropathinae radiation may have begun in the late Jurassic but trans-oceanic dispersal is required to explain the distribution of some lineages within the subfamily Macropathinae. Dating the most recent common ancestor of seven island endemic species with their nearest mainland relative suggests that each existed long before land surface on their island home was available. Main conclusions: If our molecular clock analysis is a good time estimate, then our data from the island endemic species suggest a failure to sample mainland species (New Zealand, Australia, or elsewhere) due to either extinction or lack of investment into taxonomy and species discovery.

Fast Bayesian inference of phylogenies from multiple continuous characters

Time-scaled phylogenetic trees are an ultimate goal of evolutionary biology and a necessary ingredient in comparative studies. The accumulation of genomic data has resolved the tree of life to a great extent, yet timing evolutionary events remains challenging if not impossible without external information such as fossil ages and morphological characters. Methods for incorporating morphology in tree estimation have lagged behind their molecular counterparts, especially in the case of continuous characters. Despite recent advances, such tools are still direly needed as we approach the limits of what molecules can teach us. Here, we implement a suite of state-of-the-art methods for leveraging continuous morphology in phylogenetics, and by conducting extensive simulation studies we thoroughly validate and explore our methods' properties. While retaining model generality and scalability, we make it possible to estimate absolute and relative divergence times from multiple continuous characters while accounting for uncertainty. We compile and analyze one of the most data-type diverse data sets to date, comprised of contemporaneous and ancient molecular sequences, and discrete and continuous characters from living and extinct Carnivora taxa. We conclude by synthesizing lessons about our method's behavior, and suggest future research venues.

Data from: Diversification and dispersal in the Americas revealed by new phylogenies of the wrens and allies (Passeriformes: Certhioidea)

The passerine superfamily Certhioidea lacks a complete phylogeny despite decades of recognition as a clade and extensive systematic work within all its constituent families. Here, we inferred a near-complete species level phylogeny of Certhioidea from a molecular supermatrix, including the first comprehensive sampling of the wrens (Troglodytidae), and used this phylogeny to infer its biogeographic and diversification histories. We also inferred an expanded phylogeny including nearly 100 putative phylospecies previously documented in the literature, and we found that including this diversity had notable impacts on the inferred evolutionary history of Certhioidea. This phylospecies-level tree documented a few instances of species paraphyly, some previously described in the literature and some novel. We found that Certhioidea originated largely in Eurasia and dispersed into North America five times in the last 20 million years, including at the origin of the "New World certhioids", wrens and gnatcatchers, a clade herein named Orthourae. After this initial dispersal event, both wrens and gnatcatchers diversified extensively across the hemisphere, with both lineages repeatedly crossing between continents. However, we detected no notable impact of the formation of the Isthmus of Panama on the frequency of dispersal events between North and South America. The inclusion of phylospecies altered this biogeographic inference in some portions of the tree but overall was largely consistent. With species-level sampling, we found that diversification rates within Certhioidea were largely constant through time with a detectable deceleration toward the present. By contrast, phylospecies-level sampling recovered a different diversification history with a significant rate increase at the crown node of Orthourae after dispersing into the Americas and increased speciation rates, particularly within the genera Polioptila and Henicorhina. This largely resolved phylogeny for Certhioidea has yielded important insights into the evolutionary history of this group and provides a framework for future comparative work on this fascinating clade.

opencc-zeroMar 2024View details →

Global leaf sulphur stoichiometry and the relationships with nitrogen and phosphorus: phylogeny, growth form and environmental controls

Sulphur (S) is an essential bioelement with vital roles in serving regulatory and catalytic functions, and tightly coupled with N and P in plants. However, globally stoichiometric patterns of leaf S and its relationships to leaf N and P are less well studied. We compiled 31,939 records of leaf-based data for 2,600 plant species across 6,652 sites worldwide. All plant species were divided into different phylogenetic taxa and growth forms. Standard major axis analysis was employed to fit the bivariate element relationships. A phylogenetic linear mixed effect model and a multiple regression model were used to partition the variations of bioelements into phylogeny and environments, and then to estimate the importance of environmental variables. Global geometric mean leaf S, N and P concentrations were 1.44, 15.70 and 1.27 mg g-1, with significant differences among plant groups. Leaf S-N-P positively correlated to each other, ignoring plant groups. The scaling exponents of LN-LS, LP-LS and LN-LP were 0.64, 0.76 and 0.79 for all species, but differed among plant groups. Both phylogeny and environments regulated the bioelements. The variability, rather than mean temperature controlled the bioelements. Phylogeny explained more for the concentrations of all the three bioelements than environments, of which S was the one most affected by phylogenetic taxa.

opencc-zeroMar 2024View details →

Multigenetic phylogeny of the subfamily Larentiinae (Lepidoptera: Geometridae)

This dataset is part of a paper, which demonstrates how micro-CT can be applied to provide unambiguous illustrations of diagnostic morphological characters for new taxa description and to understand how micro-CT imaging may complement other imaging techniques. Following micro-CT scanning, a semi-automatic segmentation and volume rendering protocol was used to portray the wing venation and diagnostic structures and ornamentation of male genitalia from multiple angles. Using micro-CT images, we describe a conspicuous geometrid moth from southern Africa (Lepidoptera: Geometridae), which has been present in collections since 1894 but left without an available name. Using a multigenetic dataset comprising 273 terminal taxa from the superfamily Geometroidea, we constructed a molecular phylogeny to place our study species to an isolated lineage in Geometridae: Larentiinae, tribe Xanthorhoini sensu lato. We describe it as Chloecolora vergetaria new genus, new species Englund & Staude, and provide diverse ecological information on its distribution, habitat, host plant, adult and immature stages, and parasites.

opencc-by-4.0Jun 2023View details →

Data from: Phylogeny and systematics of the "Pronophila clade", with two new genera to resolve the formerly polyphyletic genus Pseudomaniola (Lepidoptera: Nymphalidae, Satyrinae)

Analysis of a target enrichment molecular dataset confirms the monophyly of the Neotropical montane butterfly group known as the Pronophila Westwood clade, one of two major lineages of the satyrine subtribe Pronophilina. The Pronophila clade comprises 18-20 recognized genera and some 125 species. Within this group, the genus PseudomaniolaRöber appears as paraphyletic, and is split here into three genera, Pseudomaniola sensu novum with six species, including four previously considered as subspecies of P. phaselis (Hewitson), the monobasic Fahraeusia Pyrcz n. gen. for Catargynnis asuba Thieme, n. comb., and Boyeriana Pyrcz, Espeland & Willmott n. gen., with nine species. The adults of all three genera can be recognized by their wing colour patterns, but the strongest synapomorphies are found in the genitalia, especially those of the male, supporting the above systematic decisions. Notable differences are also found in scale organization and morphology. A divergence time analysis suggests that Fahraeusia diverged from Pseudomaniola +Boyeriana in the mid-Miocene, around 12 Mya, and the subsequent separation of the last two genera occurred at the start of the Pliocene at around 5 Mya.

Figure 5 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets

Figure 5. Predicted secondary structures of Pontia callidice and Pontia daplidice 22 tRNA genes.

Figure 10 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets

Figure 10. Predicted secondary structure of Pontia callidice srRNA gene.

Figure 8 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets

Figure 8. Predicted secondary structure of Talbotia naganum srRNA gene.

Figure 6 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets

Figure 6. Predicted secondary structure of Baltia butleri srRNA gene.

Figure 4 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets

Figure 4. Predicted secondary structures of Baltia butleri and Talbotia naganum 22 tRNA genes.

Figure 12 in Mitochondrial genomes of four pierid butterfly species (Lepidoptera: Pieridae) with assessments about Pieridae phylogeny upon multiple mitogenomic datasets

Figure 12. Predicted secondary structure of Pontia daplidice srRNA gene.

opencc-by-4.0Mar 2024View details →

Data for: Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but well-resolved phylogeny

Sequence alignments and gene trees for: Braun et al. "Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but well-resolved phylogeny." See README file for detailed description of all files.

opencc-zeroMar 2024View details →

A comprehensive phylogeny of Pieridae butterflies reveals a strong correlation between diversification and temperature

Temperature is thought to be a key factor influencing global species richness patterns. We investigate the link between temperature and diversification in the butterfly Family Pieridae by combining next-generation sequences and published molecular data with fine-grained distribution data. We sampled nearly 600 pierid species to build the most comprehensive molecular phylogeny of the Family and curated a distribution dataset of more than 800,000 occurrences. We found strong evidence that species in environments with more stable daily temperatures or cooler maximum temperatures in the warm seasons have higher speciation rates. Furthermore, speciation and extinction rates decreased in tandem with global temperatures through geological time, resulting in a constant net diversification.

opencc-by-nd-4.0Feb 2024View details →

Figure 8 in A deeper phylogeny of jumping spiders (Araneae: Salticidae)

Figure 8. External features of a living xiphosuran, Limulus polyphemus (original photo by James Lamsdell, after Lamsdell 2020, used under a CC BY 4.0 license). The lateral eye is a compound eye. Note the chelicerate appendages.

opencc-by-nd-4.0Feb 2024View details →

Figure 12 in A deeper phylogeny of jumping spiders (Araneae: Salticidae)

Figure 12. Structure of the epigynum in spiders (after Uhl et al. 2009). The hapogyne arrangement, with a single median gonopore serving as both the copulatory duct and ovipositor, is considered to be primitive in spiders. In the Entelegynae (grade 31), sperm is deposited by the male through a pair of copulatory ducts leading to the spermathecae, and only later passes through a pair of fertilization ducts to fertilize each egg as it passes through the medial uterus externa. A recent study (Zhan et al. 2019) has refined our understanding of the entelegyne condition, which appears to include a secondary uterus externus connnected to the two fertilization ducts leading from the sperm reservoirs (spermathecae).