Find research datasets worth reusing

opencc-zeroAug 2020View details →

Re-evaluating deep neural networks for phylogeny estimation: the issue of taxon sampling

Deep neural networks (DNNs) are powerful machine learning models that are widely used for classification problems, and have been recently proposed for quartet tree phylogeny estimation (Survorov et al. Systematic Biology 2020 and Zou et al. Molecular Biology and Evolution 2020). Here we present a study evaluating recently trained DNNs (from Zou et al., MBE 2020) in comparison to a collection of standard phylogeny estimation methods, including UPGMA, neighbor joining, maximum parsimony, and maximum likelihood, on a heterogeneous collection of 20-sequence datasets simulated under the same models that were used to train the DNNs, and also under similar conditions but with higher rates of evolution. Our study shows that using DNNs with quartet amalgamation (to combine quartet trees into a tree on the full dataset) is only more accurate than UPGMA, and otherwise is less accurate than all standard phylogeny estimation methods we explore (maximum likelihood, neighbor joining, and maximum parsimony). We further find that while DNNs can provide good quartet tree accuracy, some standard phylogeny estimation methods match or improve on DNNs for quartet accuracy, especially, but not exclusively, when used in a global manner (i.e., the tree on the full dataset is computed and then the induced quartet trees are extracted from the full tree). Thus, our study provides evidence that a major challenge impacting the utility of current DNNs for phylogeny estimation is their restriction to estimating quartet trees which must subsequently be combined into a tree on the full dataset: in contrast, global methods -- i.e., those that estimate trees from the full set of sequences -- are able to benefit from taxon sampling, and hence have higher accuracy on large datasets.

opencc-by-4.0Sep 2020View details →

Fig. 1 in Five new Palaearctic species of Docosia (Diptera: Mycetophilidae), with updated molecular phylogeny of the genus

Fig. 1. Docosia svanetica Kurina sp. nov., paratype (ZFMK-DIP-00067331), habitus.

opencc-zeroOct 2020View details →

Data from: Higher-level phylogeny and reclassification of Lampyridae (Coleoptera: Elateroidea)

Fireflies (Lampyridae) are a diverse family of beetles which exhibit an array of morphologies including varying antennal and photic organ morphologies. Due in part to their morphological diversity, the classification within the Lampyridae has long been in flux. Here we use an anchored hybrid enrichment approach to reconstruct the most extensive molecular phylogeny of Lampyridae to date (436 loci and 98 taxa) and to evaluate firefly higher-level classification. We propose several classification changes supported by morphological evidence: (1) Lamprigera, Vestini (incl. Vesta, Dodacles, Dryptelytra, and Ledocas), Photoctus, and Araucariocladus are transferred to Lampyridae incertae sedis, (2) Phausinae subfamilia nova is erected for Phausis and Lamprohiza, (3) Psilocladinae status nova is reestablished for the genus Psilocladus, (4) Pollaclasis is transferred to the Cyphonocerinae, (5) Memoan is transferred to Amydetinae, and (6) Scissicauda is transferred to Lampyrinae.

opencc-zeroNov 2020View details →

Multiple sequence alignment for the native Norwegian vascular plant phylogeny

Methods: We produced a multi-locus Maximum Likelihood (ML) phylogeny using a combination of newly produced DNA sequences from herbarium specimens and sequences available from public repositories. We combined the phylogeny with species occurrence data to estimate phylogenetic diversity and phylogenetic endemism across Norway, using a spatial randomization to judge statistical significance. We used multiple-model inference to identify environmental variables that contributed the most to the patterns of phylogenetic diversity. Finally, we estimated phylogenetic turnover and used this to identify Norwegian plant assemblages in terms of composition and evolutionary history. Results: Our ML phylogeny contained 87% of all currently described native Norwegian vascular plants. Assemblages were phylogenetically overdispersed in warmer and wetter regions of Norway, as well as in regions with a longer post-glacial history. In cold and dry regions, plant assemblages were phylogenetically clustered, and characterised by neo-endemism, while the mild and wet regions were characterised by both paleo- and neo-endemism. Phylogenetic diversity was positively correlated with summer temperature and habitat heterogeneity, and peaked in the southeast of Norway. Main conclusions: Both contemporary ecological factors (climate and habitat heterogeneity), and post-glacial history seem to have shaped the phylogenetic structure of the flora of Norway. The flora in the far north of Norway appear to be a result of recent diversification while the coastal regions are assemblages of deeper lineages. Our results suggest that there is an evolutionary signal in the distribution of the Norwegian vascular flora.

opencc-zeroNov 2020View details →

Cranial morphology of a new phytosaur (Diapsida, Archosauria) from the Upper Triassic of India: implications for phytosaur phylogeny and biostratigraphy

Detailed description and phylogenetic assessment of a phytosaur skull collected from the Tiki Formation of the Rewa Gondwana Basin of India and earlier diagnosed as Parasuchus hislopi, shows that it pertains to a new genus and species, Volcanosuchus statisticae. The new taxon is characterized by marginal overlapping of the nostrils by the antorbital fenestrae, external nares situated on a bulbous and raised dome, the lateral surface of the jugal ornamented by a prominent ridge defined by multiple tubercles and radiating thread-like structures, and distinct ornamentation patterns on the rostrum and skull table. Phylogenetic analysis nests Volcanosuchus within Mystriosuchinae where it forms a sister taxon to (Rutiodon + Leptosuchomorpha) and marks the transition between the basal Parasuchidae and more derived Mystriosuchinae phytosaurs. Evolution of the phytosaur skulls resulted in changes from non-overlapping nostril and antorbital fenestra to an overlapping state, anteroposterior elongation of the exoccipital and supraoccipital shelf, appearance of a median ridge on the basioccipital, and reduction of the supratemporal fenestra. Considerable faunal overlap of the Tiki Formation is evident with the lower Maleri Formation, which is late Carnian based on Hyperodapedon, Parasuchus, and Exaeretodon. The Tiki Formation correlates with the Ischigualasto Formation of Argentina, the upper part of the Santa Maria Formation, and the overlying lower Caturrita Formation of Brazil, the Isalo II Beds of Madagascar, Lossiemouth Sandstone of Scotland, and the lower Tecovas Formation of the Chinle Group of North America, and ranges from late Carnian to early/middle Norian.

opencc-by-4.0Dec 2020View details →

Data, Code, and Results for the Zoarcoidei Phylogeny (Hotaling et al.)

Data, code, and raw results files for a study by Hotaling et al. on Zoarcoidei phylogenetics and biogeography.

opencc-zeroJan 2021View details →

Mammalian intestinal allometry, phylogeny, trophic level and climate

An often-stated ecomorphological assumption that has the status of 'textbook knowledge' is that the dimensions of the digestive tract correlate with diet, where herbivores – consuming diets of lower digestibility – have longer intestinal tracts than faunivores – consuming diets of higher digestibility. However, statistical approaches have so far failed to demonstrate this link. Here, we collated data on the length of intestinal sections and body mass of 519 mammal species, and test for various relationships with trophic, climatic and other biological characteristics. All models showed a strong phylogenetic signal. Scaling relationships with body mass showed positive allometry at exponents >0.33, except for the caecum, which is particularly large in smaller species. Body mass was more tightly linked to small intestine than to large intestine length. Adding a diet proxy to the relationships increased model fit for all intestinal sections, except for the small intestine when accounting for phylogeny. Thus, diet has a main effect on the components of the large intestine, with longer measures in herbivores. Additionally, measures of habitat aridity had a positive relationship with large intestine length. The small intestine was longer in species from colder habitats at higher latitudes, possibly facilitating the processing of peak intake rates during the growing season. This study corroborates intuitive expectations on digestive tract anatomy, while the dependence of significant results on large sample sizes and inclusion of specific taxonomic groups indicates that the relationships cannot be considered fixed biological laws.

opencc-zeroJul 2019View details →

Data from: Ecophysiology and phylogeny of new terricolous and epiphytic chlorolichens in a fog oasis of the Atacama Desert

The Atacama Desert is one of the driest and probably oldest deserts on Earth where only a few extremophile organisms are able to survive. This study investigated two terricolous and two epiphytic lichens from the fog oasis "Las Lomitas" within the National Park Pan de Azúcar which represents a refugium for a few vascular desert plants and many lichens that can thrive on fog and dew alone. Ecophysiological measurements and climate records were combined with molecular data of the mycobiont, their green algal photobionts and lichenicolous fungi to gain information about the ecology of lichens within the fog oasis. Phylogenetic and morphological investigations led to the identification and description of the two new lichen species Ramalina reichenbergeri and Acarospora conafii as well as the lichenicolous fungi that accompanied them and revealed the trebouxioid character of all lichen photobionts. Their photosynthetic response during natural scenarios such as reactivation by high air humidity and in situ fog events were compared to elucidate the activation strategies of this lichen community. Epiphytic lichens showed photosynthetic activity that was rapidly induced by fog and additionally during high air humidity whereas terricolous lichens were only activated by fog.

opencc-zeroMar 2020View details →

Phylogeny of the Eocene Antarctic Tapetinae Gray, 1851 (Bivalvia: Veneridae) from the La Meseta and Submeseta formations

Systematic analysis shows that the Southern Hemisphere bivalve genus Retrotapes includes the Antarctic species R. antarcticus, R. newtoni, and R. robustus and recognizes for the first time the presence of Katelysia represented by K. florentinoi. Two new genera were erected in this study: Marciachlys new genus to include M. inflata new combination, and Adelfia new genus, which includes A. austrolissa new combination and A. omega new species from the Eocene of Antarctica, and the late Eocene Chilean A. arenosa new combination. Eurhomalea carlosi was synonymized with K. florentinoi; Cyclorismina marwicki with R. antarcticus; Gomphina iheringi was considered an indeterminate species; and Cockburnia lunulifera was excluded from the Tapetinae. These systematic assignments are supported by a phylogenetic analysis, which recognizes an Austral clade of Tapetinae, comprising all the genera mentioned above, and additionally Marcia, Paleomarcia, Atamarcia, and Protapes.

opencc-zeroDec 2018View details →

Data from: A multilocus phylogeny of the fish genus Poeciliopsis: solving taxonomic uncertainties and preliminary evidence of reticulation

The fish genus Poeciliopsis constitutes a valuable research system for evolutionary ecology, whose phylogenetic relationships have not been fully elucidated. We conducted a multilocus phylogenetic study of the genus based on seven nuclear and two mitochondrial loci with a thorough set of analytical approaches, i.e., concatenated (also known as super-matrix), species trees, and phylogenetic networks. Although several relationships remain unresolved, the overall results uncovered phylogenetic affinities among several members of this genus. A population previously considered of undetermined taxonomic status could be unequivocally assigned to P. scarlli; revealing a relatively recent dispersal event across the Trans Mexican Volcanic Belt (TMVB) or Pacific Ocean, which constitute a strong barrier to north-south dispersal of many terrestrial and freshwater taxa. The closest relatives of P. balsas, a species distributed south of the TMVB, are distributed in the north; representing an additional north–south split in the genus. An undescribed species of Poeciliopsis, with a highly restricted distribution (i.e., a short stretch of the Rio Concepcion; just south of the US-Mexico border), falls within the Leptorhaphis species complex. Our results are inconsistent with the hypothesis that this species originated by "breakdown" of an asexual-hybrid lineage. On the other hand, network analyses suggest one or more possible cases of reticulation within the genus that require further evaluation with genome-wide marker representation and additional analytical tools. The most strongly supported case of reticulation occurred within the subgenus Aulophallus (restricted to Central America), and implies a hybrid origin for P. retropinna (i.e., between P. paucimaculata and P. elongata). We consider that P. balsas and P. new species are of conservation concern.

Figure 6 in Phylogeny and classification of the Bucconidae (Aves, Galbuliformes) based on osteological characters

Figure 6. Phylogenetic relationships for Bucconidae species based on osteological data (Maximum Parsimony; Strict Consensus; 426 minimum steps; CI = 0,50; RI = 0,72). Numbers (1-28) indicate the nodes (branches). Values at the nodes in parentheses represent Bootstrap and Bremer indices, respectively. Red squares show the Bucco polyphyly. Illustrations of the Bucconidae species belong to the Handbook of Birds of the World – volume 7 – Bucconidae chapter (Rasmussen & Collar, 2002).

Figure 4 in Phylogeny and classification of the Bucconidae (Aves, Galbuliformes) based on osteological characters

Figure 4. Mandible: Dorsal view of N. rubecula, T. tamatia, B. capensis and H. ruficollis; caudal view of C. tenebrosa and lateral view of B. capensis and H. ruficollis. Cl + Cc = cotyla lateralis and cotyla caudalis; FACNM = fossa aditus canalis neurovascularis mandible; FcM = fossa caudalis mandibulae; PrMM = Proc. medialis mandibulae; PSM = Pars simphisialis mandibulae; RA = rostral apex of the mandible.

Figure 3 in Phylogeny and classification of the Bucconidae (Aves, Galbuliformes) based on osteological characters

Figure 3. Ventral view of the skull. Com = condylus medialis os quadratum is longer and larger; E = os ectethmoidale; FC = fossa choanalis; FM = fossa medialis; FV = fossa ventralis; P = os palatinum; PC = proeminentia cerebelaris; PrOL = proc. orbitalis os lacrimale; PrMP = proc. maxillaris os palatinum; PrPP = proc. pterigoideus os palatinum; PrRP = proc. rostrodorsalis os palatinum; PrTP = proc. transpalatinus os palatinum; PrVL = proc. ventralis os lacrimale.

Figure 2 in Phylogeny and classification of the Bucconidae (Aves, Galbuliformes) based on osteological characters

Figure 2. Lateral view of the skull. AJ = arcus jugalis; ANO = apertura nasi ossea; CrD = crista dorsalis os pterigoideus; CrV = crista ventralis os palatinum; E = os ectethmoidale; FD = facies dorsalis of the maxilla (upper jaw); FeA = fenestra anteorbitalis; FT = fossa temporalis; NM = nasal/maxillary heigth; PC = proeminentia cerebelaris; PRE = proc. esquamosalis; PrL = proc. lacrimalis; PrMN = proc. maxillaris os nasale; PrOL = proc. orbitalis os lacrimale; PrPO = proc. postorbitalis; PrTP = proc. transplatinum os palatinum; PrVL = proc. ventralis os lacrimale; TE = tuberculum os ectethmoidale; TPrPO = tuberculum of the proc. postorbitalis.

Figure 5 in Phylogeny and classification of the Bucconidae (Aves, Galbuliformes) based on osteological characters

Figure 5. Lateral view of the pelvic region of C. tenebrosa, M. rufigularis and B. capensis; dorsal view of the os sternum of B. capensis and lateral view of the os sternum of M. striata; lateral view of os tibiotarsus, tarsometatarsus and os femoris of B. capensis, T. tamatia, M. nigrifrons and H. ruficollis. F = os femoris; FG = facies gastrocnemialis os tibiotarsus; FI = foramen ilioschiadicum; IL = Incisura lateralis or fenestra lateralis; IM = incisura medialis or fenestra medialis; PrCL = proc. craniolateralis; PrDTI = proc. dorsalis terminalis ischii; SI = suclus intercnemialis; SIR = spina interna rostri; TB = os tibiotarsus; Tc = caudal tuberculum in the lateral surface of ala preacetabularis; TI = trabecula intermedia; TL = trabecula lateralis; TM = os tarsometatarsus; TS = tuberculum sulcus articularis.

Figure 1 in Phylogeny and classification of the Bucconidae (Aves, Galbuliformes) based on osteological characters

Figure 1. Dorsal view of the skull. C = concavity in the fissura zona flexoria craniofacialis; DF = depressio frontalis; F = os frontale; FC = fossa caudalis; P = os parietale; PrFL = proc. lacrimalis os frontale; PrPO = proc. postorbitalis; SFL = suture between os frontale and os lacrimalis; ZF = zona flexoria craniofacialis.

Figure 4 in Molecular phylogeny of the tribe Philodryadini Cope, 1886 (Dipsadidae: Xenodontinae): Rediscovering the diversity of the South American Racers

Figure 4. Hemipenis of Philodryas chamissonis (MNHN 3807) in A and B, Tropidodryas serra (MNRJ 7354) in C and D, and Xenoxybelis argenteus (BMNH 1994.7000) in E and F. Photographs in A, C, and E are in sulcate views, and photographs in B, D, and F are in asulcate views. Scale bars: 5 mm.

Figure 3 in Molecular phylogeny of the tribe Philodryadini Cope, 1886 (Dipsadidae: Xenodontinae): Rediscovering the diversity of the South American Racers

Figure 3. Hemipenes of Chlorosoma viridissimum (MUSM 2403) in A and B, and Incaspis amaru (FHGO 4749) in C and D. Photographs in A and C are in sulcate views, and photographs in B and D are in asulcate views. Scale bars: 5 mm.

Figure 2 in Molecular phylogeny of the tribe Philodryadini Cope, 1886 (Dipsadidae: Xenodontinae): Rediscovering the diversity of the South American Racers

Figure 2. Maximum likelihood (ML) tree estimated using RAxML, showing only the relationships of Incaspidini (1), Tropidodryadini (2), and Philodryadini (3). Terminal names on the left are presented following nomenclature in current literature, while generic and tribal arrangements on the right show our changes in the classification of Philodryadini. Numbers above and below branches indicate posterior probability and bootstrap support values, respectively. Bootstrap values below 70% and posterior probabilities below 85% are not shown.

Figure 1 in Molecular phylogeny of the tribe Philodryadini Cope, 1886 (Dipsadidae: Xenodontinae): Rediscovering the diversity of the South American Racers

Figure 1. Maximum likelihood (ML) tree of Dipsadidae estimated using RAxML. Summary tree with collapsed terminals showing higher-level relationships. Numbers above and below branches indicate bootstrap and posterior probability support values, respectively. Bootstrap values below 70% and posterior probabilities below 85% are not shown. Abbreviations: CA = central Andean; SAE = southern and cis-Andean.