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The evolutionary history of Neanderthal and Denisovan Y chromosomes
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The genomes of archaic hominins have been sequenced and compared with that of modern humans. However, most archaic individuals with high-quality sequences available have been female. Petr et al. performed targeted sequencing of the paternally inherited Y chromosomes from three Neanderthals and two Denisovans (see the Perspective by Schierup). Comparisons with available archaic and diverse modern human Y chromosomes indicated that, similar to the maternally inherited mitochondria, the human and Neanderthal Y chromosomes were more closely related to each other compared with the Denisovan Y chromosome. This result supports the conclusion that interbreeding between early humans and Neanderthals and selection replaced the more ancient Denisovian-like Y chromosome and mitochondria in Neanderthals.Science, this issue p. 1653; see also p. 1565Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans.
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RBINS Staff Publications 2020
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A century of coping with environmental and ecological changes via compensatory biomineralization in mussels
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RBINS Staff Publications 2021
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On two new species of Cypricercus Sars 1895 (Crustacea, Ostracoda) from Brazil
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We describe two new species of Cypricercus, Cypricercus alfredo sp. nov. and Cypricercus tiao sp. nov., and briefly redescribe the female of Cypricercus centrurus (Klie, 1940) from Brazilian floodplains. Both new species have the elongated carapace which is characteristic of the genus. Cypricercus alfredo sp. nov. was found as both sexual and asexual populations and has a posterior spine on the right valve and differs from the Brazilian C. centrurus by the position and the size of spine and the size and shape of the carapace. Cypricercus tiao sp. nov. was found as one asexual population only and lacks a posterior spine on the right valve. Cypricercus populations in Brazil mostly consist exclusively of asexual females, but some sexual populations and populations with mixed reproduction can also be found. This genus occurs primarily in the Southern Hemisphere, but some species can also be found in the southern part of North America and in India. We also present a re-appraisal of all species presently allocated to the genus, primarily based on original descriptions.
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RBINS Staff Publications 2021
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Species niches, not traits, determine abundance and occupancy patterns: A multi‐site synthesis
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Aim Locally abundant species are usually widespread, and this pattern has been related to properties of the niches and traits of species. However, such explanations fail to account for the potential of traits to determine species niches and often overlook statistical artefacts. Here, we examine how trait distinctiveness determines the abilities of species to exploit either common habitats (niche position) or a range of habitats (niche breadth) and how niche position and breadth, in turn, affect abundance and occupancy. We also examine how statistical artefacts moderate these relationships. Location Sixteen sites in the Neotropics. Time period 1993–2014. Major taxa studied Aquatic invertebrates from tank bromeliads. Methods We measured the environmental niche position and breadth of each species and calculated its trait distinctiveness as the average trait difference from all other species at each site. Then, we used a combination of structural equation models and a meta-analytical approach to test trait–niche relationships and a null model to control for statistical artefacts. Results The trait distinctiveness of each species was unrelated to its niche properties, abundance and occupancy. In contrast, niche position was the main predictor of abundance and occupancy; species that used the most common environmental conditions found across bromeliads were locally abundant and widespread. Contributions of niche breadth to such patterns were attributable to statistical artefacts, indicating that effects of niche breadth might have been overestimated in previous studies. Main conclusions Our study reveals the generality of niche position in explaining one of the most common ecological patterns. The robustness of this result is underscored by the geographical extent of our study and our control of statistical artefacts. We call for a similar examination across other systems, which is an essential task to understand the drivers of commonness across the tree of life.
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RBINS Staff Publications 2021
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The value of eco-volunteer projects for biodiversity conservation-butterfly monitoring in Krka National Park (Croatia) with an updated checklist.
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The biogeographical importance of Dalmatia, bordered by the Dinaric Alps and the Adriatic Sea, is evident through the rich biodiversity of this region and its network of protected areas. One of those areas, Krka National Park (NP), supports a wide range of natural habitats, but rapidly increasing tourism puts high pressure on its ecosystems, despite its protected status. Accurate knowledge of species and their distributions within natural places such as Krka is essential to direct and prioritize future conservation efforts. As collecting biodiversity data is time and resource-intensive, alternative ways to obtain this information are needed. One possibility is monitoring based on ecovolunteering. From June to August of 2019, an Operation Wallacea/BIOTA scientific team surveyed a section of Krka NP and its surrounding boundaries, within the vicinity of the village of Puljane, to study its butterfly richness and abundance. Pollard walks and static count surveys were conducted with the help of eco-volunteers, testing the effectiveness of gathering field data through this approach. Overall, 57 butterfly species were found throughout the study, including four new records for Krka NP. Three further new species for the park were detected close to its boundaries and are also expected to occur within its borders. Here, we present an updated butterfly checklist for Krka NP, highlighting the positive impact of eco-volunteering initiatives and the importance of combined research efforts to study and protect the rich biodiversity and ecosystems of protected areas.
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RBINS Staff Publications 2021
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Climate influences the response of community functional traits to local conditions
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Functional traits determine an organism’s performance in a given environment and as such determine which organisms will be found where. Species respond to local conditions, but also to larger scale gradients, such as climate. Trait ecology links these responses of species to community composition and species distributions. Yet, we often do not know which environmental gradients are most important in determining community trait composition at either local or biogeographical scales, or their interaction. Here we quantify the relative contribution of local and climatic conditions to the structure and composition of functional traits found within bromeliad invertebrate communities. We conclude that climate explains more variation in invertebrate trait composition within bromeliads than does local conditions. Importantly, climate mediated the response of traits to local conditions; for example, invertebrates with benthic life-history traits increased with bromeliad water volume only under certain precipitation regimes. Our ability to detect this and other patterns hinged on the compilation of multiple fine-grained datasets, allowing us to contrast the effect of climate vs. local conditions. We suggest that, in addition to sampling communities at local scales, we need to aggregate studies that span large ranges in climate variation in order to fully understand trait filtering at local, regional and global scales.
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RBINS Staff Publications 2021
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Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing
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Background Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. Results In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. Conclusions Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.
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RBINS Staff Publications 2021
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Species' traits and taxonomic distance can predict the hatching phenology of ostracod (Crustacea) resting eggs from tropical floodplain lakes
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Freshwater ostracods are commonly found in temporary ponds and lakes, surviving drought periods by producing resting eggs. We investigated the hatching phenology of ostracod resting eggs from the sediments of temporary floodplain lakes, considering both the taxonomic distance between species and their functional traits, such as carapace size (length and height) and shape, valve ornamentation, and reproductive mode. In addition, we tested the hypotheses: (1) that the hatching time is more similar between congeneric ostracod species than between noncongeneric species; (2) that differences in hatching time between congeneric species are often related to differences in functional traits; (3) that both species composition and functional traits composition of hatchlings change over the incubation time, but with a reduction in the variability over time. The experiment was conducted for 98 days in the laboratory, and the microcosms were monitored weekly. The first hatching of an ostracod was recorded during the second week of incubation after hydration of the sediments. A total of 12 ostracod species hatched, belonging to the families Cyprididae and Candonidae. The above three hypotheses were corroborated. The time between inundation and first hatching was mostly similar for congeneric species in the genus Chlamydotheca, but was different between some species of Strandesia, which might be owing to differences in functional traits. The species composition and functional trait composition of the hatched ostracods were significantly different over the 14 weeks of incubation due to the different hatching phenology of different species. Furthermore, our results show that both taxonomic distance and functional traits can influence the hatching time of ostracod resting eggs from temporary floodplain lakes. Thus, future studies addressing the hatching phenology of ostracod resting eggs (and resting stages from other invertebrates) should also emphasize the use of functional traits.
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RBINS Staff Publications 2021
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A new tribe, two new genera and three new species of Cypridopsinae (Crustacea, Ostracoda, Cyprididae) from Brazil.
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We describe one new tribe, two new genera and three new species of the subfamily Cypridopsinae Kaufmann, 1900 from Brazilian floodplains. Brasilodopsis gen. nov. belongs in the nominal tribe Cypridopsini, and both new species in this new genus were found in both sexual and asexual populations. Brasilodopsis baiabonita gen. et sp. nov. has a wide distribution and was found in three of the four major Brazilian floodplains. Brasilodopsis amazonica gen. et sp. nov. was recorded only from the Amazon floodplain. Brasilodopsis baiabonita gen. et sp. nov. has a subtriangular shape in lateral view, whereas Brasilodopsis amazonica gen. et sp. nov. is more elongated and has more rounded dorsal margins in both valves, as well as more pronounced external valve ornamentation, consisting of rimmed pores in shallow pits. Paranadopsis reducta gen. et sp. nov. was found in asexual populations in the Upper Paraná River floodplain only and differs from other Cypridopsinae in the more elongated carapace, an A1 with strongly reduced chaetotaxy (hence the specific name) and the total absence of caudal rami in females. Because of these strong reductions in valve and limb morphology, Paranadopsini trib. nov. is created within the Cypridopsinae for this intriguing new genus and species.
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RBINS Staff Publications 2021
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The representativeness of protected areas for Amazonian fish diversity under climate change.
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RBINS Staff Publications 2021
