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opencc-zeroMay 2020View details →

Data from: A multilocus analysis of Epicopeiidae (Lepidoptera, Geometroidea) provides new insights into their relationships and the evolutionary history of mimicry

The family Epicopeiidae is a small group of day-flying moths, known for mimicking many different groups of butterflies and moths. So far, there still lacks a reliable phylogenetic framework of Epicopeiidae that is necessary to our understanding of the evolutionary process of their mimicry. In this study, we sequenced 94 nuclear protein-coding markers for 56 epicopeiid samples and 11 outgroups, covering all ten genera of Epicopeiidae. We used homemade PCR-generated baits to capture target sequences, which allowed us to utilize old and dried specimens that were difficult to handle by conventional PCR + Sanger sequencing. Maximum likelihood and Bayesian analyses of the newly obtained dataset (86,388 bp) at both DNA and protein levels produced identical phylogenies with strong support. The non-mimicry genus Deuveia is the sister group of other epicopeiid genera. Epicopeia and Nossa are not monophyletic, and these two genera nest together to form a clade. We also estimated divergence times of Epicopeiidae and found that their initial diversification happened in Eocene about 41 million years ago. The ancestral state reconstruction of mimicry type for this family suggested that the last common ancestor of epicopeiid moths is non-mimetic, and the Riodinidae-mimicry type evolved first. In summary, our work provides a comprehensive and robust time-calibrated phylogeny of Epicopeiidae that provides a sound framework for revising their classification and interpreting character evolution.

opencc-zeroJul 2020View details →

Data from: Inducing seed dispersal by generalist frugivores: A new technique to overcome dispersal limitation in restoration

1. Dispersal limitation severely impairs the trajectory of restoration, mainly due to the lack of seed vectors bringing seeds from nearby habitats; a role played by many frugivorous vertebrates that can be absent or reduced in restored or degraded sites. 2. Here we propose a new technique named Induced Seed Dispersal, that amplifies the role that many generalist frugivores have in seed dispersal. It consists in the offering of seeds embedded in the pulp of commercial fruits or whole native fleshy fruits in feeders to generalist frugivores, which ingest the seeds and defecate them elsewhere. We set feeders in a restored site and monitored the visiting pattern of these frugivores with cameras-traps. We also set seed traps to retrieve seeds dispersed by frugivores and offered around 1500 seeds of Cecropia hololeuca (Urticaceae) per week for one year. 3. We recorded at least 24 generalist frugivore species of terrestrial mammals, bats, and birds, which ingested/removed the seeds/fruits from the feeders. Seeds of C. hololeuca dispersed by marmosets were retrieved in the seed traps and germinated. We estimated a potential seed rain of more than 600 C. hololeuca seeds ha-1 mo-1. 4. Synthesis and applications. Our study demonstrates that this new technique can make use of generalist frugivores to assist restoration or regeneration into sites where seed dispersal is compromised by the lack of dispersers or limited seed arrival. Inducing seed dispersal by generalist frugivores is a low-cost and easy-managed technique that can be applied year-round in restoration and forest enrichments at all scales.

Data from: Vasohibin1, a new IRES trans-acting factor for induction of (lymph)angiogenic factors in early hypoxia

Hypoxia, a major inducer of angiogenesis, triggers major changes of gene expression at the transcriptional level. Furthermore, global protein synthesis is blocked while internal ribosome entry sites (IRES) allow specific mRNAs to be translated. Here we report the transcriptome and translatome signatures of (lymph)angiogenic genes in hypoxic HL-1 cardiomyocytes: most genes are not induced at the transcriptome-, but at the translatome level, including all IRES-containing mRNAs. Our data reveal activation of (lymph)angiogenic factor mRNA IRESs in early hypoxia. We identify vasohibin1 (VASH1) as an IRES trans-acting factor (ITAF) able to bind RNA and to activate FGF1 and VEGFD IRESs in hypoxia while it exhibits an inhibitory effect in normoxia. This suggests a generalized process of IRES-dependent induction of (lymph)angiogenic growth factors in early hypoxia, with a variable IRESome composition. IRES-dependent translation thus appears as a pivotal process to trigger new vessel formation in ischemic heart.

opencc-zeroMay 2021View details →

Data from: Fluid preservation causes minimal reduction of parasite detectability in fish specimens: a new approach for reconstructing parasite communities of the past?

<ol> <li>Long-term datasets are needed to evaluate temporal patterns in wildlife disease burdens, but historical data on parasite abundance are extremely rare. For more than a century, natural history collections have been accumulating fluid-preserved specimens, which should contain the parasites infecting the host at the time of its preservation. However, before this unique data source can be exploited, we must identify the artefacts that are introduced by the preservation process. Here, we experimentally address whether the preservation process alters the degree to which metazoan parasites are detectable in fluid-preserved fish specimens when using visual parasite detection techniques.</li> <li>We randomly assigned fish of three species (Gadus chalcogrammus, Thaleichthys pacificus, Parophrys vetulus) to two treatments. In the first treatment, fish were preserved according to the standard procedures used in ichthyological collections. Immediately after the fluid-preservation process was complete, we performed parasitological dissection on those specimens. The second treatment was a control, in which fish were dissected without being subjected to the fluid-preservation process. We compared parasite abundance between the two treatments.</li> <li>Across 298 fish individuals and 59 host–parasite pairs, we found few differences between treatments, with 24 of 27 host–parasite pairs equally abundant between the two treatments. Of these, one pair was significantly more abundant in the preservation treatment than in the control group, and two pairs were significantly less abundant in the preservation treatment than in the control group.</li> <li>Our data suggest that the fluid-preservation process does not have a substantial effect on the detectability of metazoan parasites. This study addresses only the effects of the fixation and preservation process; long-term experiments are needed to address whether parasite detectability remains unchanged in the months, years, and decades of storage following preservation. If so, ecologists will be able to reconstruct novel, long-term datasets on parasite diversity and abundance over the past century or more using fluid-preserved specimens from natural history collections.</li> </ol>

Data from: Appearances can be deceptive: bizarre shell microanatomy and histology in a new Triassic turtle (Testudinata) from Argentina at the dawn of turtles

The origin and homology of the turtle shell are one of the most captivating topics in amniote evolution. In this contribution, we present a new species of turtle from the Late Triassic of Argentina whose peripheral plates question the homology of these bones in turtles. The external morphology of the peripheral plates of Waluchelys cavitesta gen. et sp. nov. (Testudinata: Australochelyidae) is as in any other turtle, however, appearances can be deceiving. Internally, these plates exhibit an unexpected internal cavity. The absence of structural similarities and of ontogenetic or phylogenetic transitional forms between the peripheral plates of W. cavitesta and other testudinatans might suggest that the periphery of turtles represents a case of deep homology. Furthermore, the present and recent findings suggest that the structure and ossification patterns of the periphery of the turtle shell were more plastic and subject to variation than other elements of the shell, at least in the earliest stages of turtle evolution. These findings also suggest that the "typical" mesochelydian turtle shell could have been acquired in a two-stage process.

Data from: Novel track morphotypes from new tracksites indicate increased Middle Jurassic dinosaur diversity on the Isle of Skye Scotland

Dinosaur fossils from the Middle Jurassic are rare globally, but the Isle of Skye (Scotland, UK) preserves a varied dinosaur record of abundant trace fossils and rare body fossils from this time. Here we describe two new tracksites from Rubha nam Brathairean (Brothers' Point) near where the first dinosaur footprint in Scotland was found in the 1980s. These sites were formed in subaerially exposed mudstones of the Lealt Shale Formation of the Great Estuarine Group and record a dynamic, subtropical, coastal margin. These tracksites preserve a wide variety of dinosaur track types, including a novel morphotype for Skye: Deltapodus which has a probable stegosaur trackmaker. Additionally, a wide variety of tridactyl tracks shows evidence of multiple theropods of different sizes and possibly hints at the presence of large-bodied ornithopods. Overall, the new tracksites show the dinosaur fauna of Skye is more diverse than previously recognized and give insight into the early evolution of major dinosaur groups whose Middle Jurassic body fossil records are currently sparse.

Data from: The multilocus multispecies coalescent: a flexible new model of gene family evolution

Incomplete lineage sorting (ILS), the interaction between coalescence and speciation, can generate incongruence between gene trees and species trees, as can gene duplication (D), transfer (T) and loss (L). These processes are usually modelled independently, but in reality, ILS can affect gene copy number polymorphism, i.e., interfere with DTL. This has been previously recognised, but not treated in a satisfactory way, mainly because DTL events are naturally modelled forward-in-time, while ILS is naturally modelled backwards-in-time with the coalescent. Here we consider the joint action of ILS and DTL on the gene tree/species tree problem in all its complexity. In particular, we show that the interaction between ILS and duplications/transfers (without losses) can result in patterns usually interpreted as resulting from gene loss, and that the realised rate of D, T and L becomes non-homogeneous in time when ILS is taken into account. We introduce algorithmic solutions to these problems. Our new model, the multilocus multispecies coalescent (MLMSC), which also accounts for any level of linkage between loci, generalises the multispecies coalescent model and offers a versatile, powerful framework for proper simulation and inference of gene family evolution.

Data from: Lithobieae and Eriocnemeae: two new neotropical tribes of Melastomataceae

Lithobium is a monotypic genus in the Melastomataceae restricted to southeastern Brazil. Most previous students of the family have placed these diminutive herbs into the Microlicieae, but some classifications have assigned the genus to the Sonerileae or Bertolonieae. Eriocnema is also a monotypic genus that has been included in the Bertolonieae, Sonerileae, and also Microlicieae. Ochthephilus, yet another monotypic genus, was assigned to the Merianieae, but lack of fruits and seeds, and a paucity of collections, have made it difficult to correctly place in a phylogenetic context. In this phylogenetic analysis, 91 species representing 73 genera from across the Melastomataceae, including 24 of the 27 genera putatively closely related to Lithobium, Eriocnema, Ochthephilus, and Physeterostemon were sampled for seven molecular markers, i.e., the nuclear ribosomal external transcribed spacer region (ETS) and internal transcribed spacer region (ITS), the plastid accD–psaI spacer region, ndhF, psbK–psbL, rbcL, and rpl16. Lithobium is on an isolated branch and is not a member of any other clade, thus a new tribe, Lithobieae, is proposed to accommodate it. In this analysis, Eriocnema and Ochthephilus form a clade including Physeterostemon that is sister to the Miconieae and separate from tribes that they have been associated with in historical classifications, thus another new tribe, Eriocnemeae, is proposed.

Data for: Psychological distress, anxiety, suicidality, and wellbeing in New Zealand during the COVID-19 lockdown: a cross-sectional study

Dataset for following paper. Introduction New Zealand's early response to the novel coronavirus pandemic included a strict lockdown which eliminated community transmission of COVID-19. However, this success was not without cost, both economic and social. In our study, we examined the psychological wellbeing of New Zealanders during the COVID-19 lockdown when restrictions reduced social contact, limited recreation opportunities, and resulted in job losses and financial insecurity. Methods We conducted an online panel survey of a demographically representative sample of 2010 adult New Zealanders. The survey contained three standardised measures – the Kessler Psychological Distress Scale (K10), the GAD-7, and the Well-Being Index (WHO-5) – as well as questions designed specifically to measure family violence, suicidal ideation, and alcohol consumption. It also included items assessing positive aspects of the lockdown. Results Thirty percent of respondents reported moderate to severe psychological distress (K10), 16% moderate to high levels of anxiety, and 39% low wellbeing; well above baseline measures. Poorer outcomes were seen among young people and those who had lost jobs or had less work, those with poor health status, and who had past diagnoses of mental illness. Suicidal ideation was reported by 6%, with 2% reporting making plans for suicide and 2% reporting suicide attempts. Suicidality was highest in those aged 18–34. Just under 10% of participants had directly experienced some form of family harm over the lockdown period. However, not all consequences of the lockdown were negative, with 64% reporting 'silver linings', which included enjoying working from home, spending more time with family, and a quieter, less polluted environment. Conclusions New Zealand's lockdown successfully eliminated COVID-19 from the community, but our results show this achievement brought a significant psychological toll. Although much of the debate about lockdown measures has focused on their economic effects, our findings emphasise the need to pay equal attention to their effects on psychological wellbeing.

opencc-zeroOct 2019View details →

Data from: New and Old World phylogeography of pumpkinseed (Lepomis gibbosus): the North American origin of introduced populations in Europe

To determine the origin of introduced European populations of pumpkinseed (Lepomis gibbosus) – a freshwater sunfish, native to eastern North America that has spread across western and central Europe – we investigated the phylogeography of the species by sequencing the mitochondrial NADH subunit 1 gene. A total of 543 pumpkinseed were sampled from 32 sites across the native range of the species, and from 19 sites covering much of its introduced European range. The presence and geographic distribution of two distinct clades in North American populations were discovered, suggesting that pumpkinseed survived the Pleistocene glaciations in two refugia (Atlantic and Mississippian). Analyses of mitochondrial variation revealed that European pumpkinseed may have been introduced to Europe from at least two distinct sources, but from the Atlantic drainages of North America only, which is consistent with historical records. Within Europe, haplotype distributions of pumpkinseed lend support to the entry of non-native fishes into Iberia via the so-called 'Perpignan–Barcelona corridor'. European populations possessed lower genetic diversity than populations from North America, suggesting that low genetic diversity may not preclude a species from establishing and spreading into new environments outside of their native range.

Data from: New material of Gobicyon (Carnivora, Amphicyonidae, Haplocyoninae) from northern China and a review of Aktaucyonini evolution

The aberrant carnivore Gobicyon has been known for more than 80 years, but the evolutionary position and taxonomic diversity of this animal remain unclear due to the paucity of the known fossils. Here, we report a much richer and better preserved assemblage of Gobicyon material from Tongxin and Hezheng areas, northern China. Two new species, Gobicyon yei sp. nov. from the early Middle Miocene in Tongxin area and Gobicyon acutus sp. nov. from the late Middle Miocene in Hezheng area were recognised. Much better material of Gobicyon macrognathus and one isolated tooth of Gobicyon zhegalloi from Tongxin area are also described in detail. Gobicyon is recognised as a derived haplocyonid. A phylogenetic analysis of Gobicyon and related taxa was performed for the first time. The phylogenetic tree suggests a close relationship of Aktaucyon and Gobicyon (Aktaucyonini). Among the taxa traditionally included in haplocyonids, Haplocyonopsis is the closest to Aktaucyonini, as supported by its centrally located M1 protocone and a uniformly distributed M1 lingual cingulum. The most significant evolutionary trends of Gobicyon are the reduction of the posterior molars (M2 and M3) and the strengthening of P4 and M1, suggesting a forward shift of crushing function along the tooth row.

New insights into the patterns and drivers of avian altitudinal migration from a growing crowdsourcing data source

Altitudinal migration is a common and important but understudied behavior in birds. Difficulty in characterizing avian altitudinal migration has prevented a comprehensive understanding of this behavior. To address this, we investigated the altitudinal migration patterns and explored potential drivers for a major proportion (~70%) of the entire resident bird community along an almost 4,000 m elevational gradient on the main island of Taiwan. Based on the occurrence records collected by citizen scientists, we examined the seasonal shifts in the center and the upper and lower boundaries of elevational distributions for 104 individual species. We then built phylogeny-controlled regression models to investigate the associations between the birds' seasonal distribution shifts and seven of their traits, and examined whether the observed shifts can be explained by three main hypotheses on potential drivers. Results showed that at least 60 species (58%) seasonally changed their distributions along elevations. While most of them (42 species) tended to move downhill in winter, a considerable number of species (14) tended to move uphill. While the species breeding at high or low elevations tended to move downhill in winter, those breeding at medium-low elevations tended to move or extend their distributions to higher elevations. Our regression models suggested that seasonal variations in climates and food availability could be major drivers of the behavior. However, the three hypotheses can only partially explain the observed downhill migration patterns and none of them can well explain the uphill patterns, indicating an important knowledge gap. This study investigated avian altitudinal migration from a new perspective with a novel and generalizable approach, and revealed interesting patterns that could be difficult to identify with conventional approaches. It demonstrated the power of citizen science data to provide new insights into this behavior by characterizing the general patterns and mechanisms across a large number of species.

Data from: A taxonomic revision of the whitefish radiation of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei: Coregonidae)

The alpha taxonomy of the endemic whitefish of lakes Brienz and Thun, Switzerland, is revised. We evaluate the status of seven known species: Coregonus steinmanni sp. nov., Coregonus profundus sp. nov. and Coregonus acrinasus sp. nov. are endemic to Lake Thun; Coregonus brienzii sp. nov. is endemic to Lake Brienz; and C. alpinus, C. albellus, and C. fatioi from lakes Brienz and Thun are redescribed. One of these species, C. alpinus, is revised, since the lectotype for this species is incongruent with the species description given by Kottelat (1997) and Kottelat and Freyhof (2007). The name C. alpinus is thus retained for the lectotype designated by Kottelat (1997) and a new description of this taxon provided. For the species otherwise described by Kottelat (1997) and Kottelat and Freyhof (2007) as C. alpinus the new name C. profundus is designated. Coregonus acrinasus is genetically partially of allochthonous origin, closely related to the radiation of Lake Constance, and we therefore compare it to all recognized species of Lake Constance, C. wartmanni, C. macrophthalmus, C. arenicolus, and C. gutturosus.

Data from: The history of tree and shrub taxa on Bol'shoy Lyakhovsky Island (New Siberian Archipelago) since the last interglacial uncovered by sedimentary ancient DNA and pollen data

Ecosystem boundaries, such as the Arctic-Boreal treeline, are strongly coupled with climate and were spatially highly dynamic during past glacial-interglacial cycles. Only a few studies cover vegetation changes since the last interglacial, as most of the former landscapes are inundated and difficult to access. Using pollen analysis and sedimentary ancient DNA (sedaDNA) metabarcoding, we reveal vegetation changes on Bol'shoy Lyakhovsky Island since the last interglacial from permafrost sediments. Last interglacial samples depict high levels of floral diversity with the presence of trees (Larix, Picea, Populus) and shrubs (Alnus, Betula, Ribes, Cornus, Saliceae) on the currently treeless island. After the Last Glacial Maximum, Larix re-colonised the island but disappeared along with most shrub taxa. This was probably caused by Holocene sea-level rise, which led to increased oceanic conditions on the island. Additionally, we applied two newly developed larch-specific chloroplast markers to evaluate their potential for tracking past population dynamics from environmental samples. The novel markers were successfully re-sequenced and exhibited two variants of each marker in last interglacial samples. SedaDNA can track vegetation changes as well as genetic changes across geographic space through time and can improve our understanding of past processes that shape modern patterns.

opencc-zeroOct 2020View details →

Data from: A new Devonian euthycarcinoid evidences the use of different respiratory strategies during the marine-to-terrestrial transition in the myriapod lineage

Myriapods were, together with arachnids, the earliest animals to occupy terrestrial ecosystems, by at least the Silurian. The origin of myriapods and their land colonization have long remained puzzling until euthycarcinoids, an extinct group of aquatic arthropods considered amphibious, were shown to be stem group myriapods, extending the lineage to the Cambrian and evidencing a marine-to-terrestrial transition. Although possible respiratory structures comparable to the air-breathing tracheal system of myriapods are visible in several euthycarcinoids, little is known about the mechanism by which they respired. Here we describe a new euthycarcinoid from Upper Devonian alluvio-lagoonal deposits of Belgium. Synchrotron-based elemental x-ray analyses were used to extract all available information from the only known specimen. Sulfur x-ray fluorescence (XRF) mapping and spectroscopy unveil sulphate evaporation stains, spread over the entire slab, suggestive of a very shallow-water to terrestrial environment prior to burial consistent with an amphibious lifestyle. Trace metal XRF mapping reveals a pair of ventral spherical cavities or chambers on the second post-abdominal segment that do not compare to any known feature in aquatic arthropods, but might well play a part in air-breathing. Our data provide additional support for amphibious lifestyle in euthycarcinoids and show that different respiratory strategies were used during the marine-to-terrestrial transition in the myriapod lineage.

opencc-zeroNov 2020View details →

Data from: Constrained optimization of landscape indices in conservation planning to support ecological restoration in New Caledonia

1. Curbing habitat loss, reducing fragmentation, and restoring connectivity are frequent concerns of conservation planning. In this respect, the incorporation of spatial constraints, fragmentation, and connectivity indices into optimization procedures is an important challenge for improving decision support. 2. Here we present a novel optimization approach developed to accurately represent a broad range of conservation planning questions with spatial constraints and landscape indices. Relying on constraint programming, a technique from artificial intelligence based on automatic reasoning, this approach provides both constraint satisfaction and optimality guarantees. 3. We applied this approach in a real case study to support managers of the ``Côte Oubliée -- `Woen Vùù -- Pwa Pereeù'' provincial park project, in the biodiversity hotspot of New Caledonia. Under budget, accessibility, and equitable allocation constraints, we identified restorable areas optimal for reducing forest fragmentation and improving inter-patch structural connectivity, respectively measured with the effective mesh size and the integral index of connectivity. 4. Synthesis and applications. Our work contributes to more effective and policy-relevant conservation planning by providing a spatially-explicit and problem-focused optimization approach. By allowing an exact representation of spatial constraints and landscape indices, it can address new questions and ensure whether the solutions will be socio-economically feasible, through optimality and satisfiability guarantees. Our approach is generic and flexible, thus applicable to a wide range of conservation planning problems such as ecological restoration planning, reserve or corridor design.