Mapping the Constrained Coding Regions in the Human Genome to Their Corresponding Proteins

Constrained Coding Regions (CCRs) in the human genome have been derived from DNA sequencing data of large cohorts of healthy control populations, available in the Genome Aggregation Database (gnomAD) [1]. They identify regions depleted of protein-changing variants and thus identify segments of the genome that have been constrained during human evolution. By mapping these DNA-defined regions from genomic coordinates onto the corresponding protein positions and combining this information with protein annotations, we have explored the distribution of CCRs and compared their co-occurrence with different protein functional features, previously annotated at the amino acid level in public databases.As expected, our results reveal that functional amino acids involved in interactions with DNA/RNA, protein–protein contacts and catalytic sites are the protein features most likely to be highly constrained for variation in the control population. More surprisingly, we also found that linear motifs, linear interacting peptides (LIPs), disorder–order transitions upon binding with other protein partners and liquid–liquid phase separating (LLPS) regions are also strongly associated with high constraint for variability. We also compared intra-species constraints in the human CCRs with inter-species conservation and functional residues to explore how such CCRs may contribute to the analysis of protein variants. As has been previously observed, CCRs are only weakly correlated with conservation, suggesting that intraspecies constraints complement interspecies conservation and can provide more information to interpret variant effects.     

Two decades of genetic profiling yields first evidence of natal philopatry and long‐term fidelity to parturition sites in sharks

Sharks are a globally threatened group of marine fishes that often breed in their natal region of origin. There has even been speculation that female sharks return to their exact birthplace to breed (‘natal philopatry’), which would have important conservation implications. Genetic profiling of lemon sharks (Negaprion brevirostris) from 20 consecutive cohorts (1993–2012) at Bimini, Bahamas, showed that certain females faithfully gave birth at this site for nearly two decades. At least six females born in the 1993–1997 cohorts returned to give birth 14–17 years later, providing the first direct evidence of natal philopatry in the chondrichthyans. Long‐term fidelity to specific nursery sites coupled with natal philopatry highlights the merits of emerging spatial and local conservation efforts for these threatened predators.     

Incorporating latitudinal and central–marginal trends in assessing genetic variation across species ranges

The genetic variation across a species’ range is an important factor in speciation and conservation, yet searching for general patterns and underlying causes remains challenging. While the majority of comparisons between central and marginal populations have revealed a general central–marginal (C–M) decline in genetic diversity, others show no clear pattern. Similarly, most latitudinal studies (although much fewer, especially those conducted rangewide) also showed latitudinal trends in genetic variation. To date, the C–M and latitudinal patterns have often been examined independently and have rarely been considered together when accounting for the observed genetic variation across species ranges. Here, in the light of the most recent findings, I show how latitude might be responsible for some of the deviations from the general C–M trends in genetic diversity, and vice versa. In the future, integrating latitude and range geometry with climate‐induced species migration would offer important insights into conservation prioritization across species ranges.     

The conservation profile of a protein bears the imprint of the molecule that is evolutionarily coupled to the protein

The conservation profile of a protein is a curve of the conservation levels of amino acids along the sequence. Biologists are usually more interested in individual points on the curve (namely, the conserved amino acids) than the overall shape of the curve. Here, we show that the conservation curves of proteins bear the imprints of molecules that are evolutionarily coupled to the proteins. Our method is based on recent studies that a sequence conservation profile is quantitatively linked to its structural packing profile. We find that the conservation profiles of nucleic acid (NA) binding proteins are better correlated with the packing profiles of the protein–NA complexes than those of the proteins alone. This indicates that a nucleic acid binding protein evolves to accommodate the nucleic acid in such a way that the residues involved in binding have their conservation levels closely coupled with the specific nucleotides. Proteins 2015; 83:1407–1413. © 2015 Wiley Periodicals, Inc.     

Dispersal and gene flow in the rare, parasitic Large Blue butterfly Maculinea arion

Dispersal is crucial for gene flow and often determines the long‐term stability of meta‐populations, particularly in rare species with specialized life cycles. Such species are often foci of conservation efforts because they suffer disproportionally from degradation and fragmentation of their habitat. However, detailed knowledge of effective gene flow through dispersal is often missing, so that conservation strategies have to be based on mark–recapture observations that are suspected to be poor predictors of long‐distance dispersal. These constraints have been especially severe in the study of butterfly populations, where microsatellite markers have been difficult to develop. We used eight microsatellite markers to analyse genetic population structure of the Large Blue butterfly Maculinea arion in Sweden. During recent decades, this species has become an icon of insect conservation after massive decline throughout Europe and extinction in Britain followed by reintroduction of a seed population from the Swedish island of Öland. We find that populations are highly structured genetically, but that gene flow occurs over distances 15 times longer than the maximum distance recorded from mark–recapture studies, which can only be explained by maximum dispersal distances at least twice as large as previously accepted. However, we also find evidence that gaps between sites with suitable habitat exceeding ～20 km induce genetic erosion that can be detected from bottleneck analyses. Although further work is needed, our results suggest that M. arion can maintain fully functional metapopulations when they consist of optimal habitat patches that are no further apart than ～10 km.     

Current status and future directions of applied behavioral research for animal welfare and conservation

The papers that follow in this special issue reflect the state of knowledge and theory in the fields of animal welfare and conservation behavior. A particular focus is placed on how enrichment can be used judiciously to improve welfare and to prepare captive animals for release back to the wild. However, my purpose here is not simply to reiterate what the contributors of this special issue have said, but to provide an overview of the major themes, problems, and opportunities in applied animal behavior related to conservation and welfare. I review major issues in three interrelated areas: captive welfare, captive breeding, and conservation behavior research for wild populations. Despite many advancements in welfare science, one of the most significant impediments to a predictive science of welfare is the need to further refine theories advanced to explain environment–welfare relationships. I provide a brief overview of ten theories that have been proposed to explain good or poor welfare and suggest that they need to be made more conceptually distinct so that clear hypotheses can be articulated, and predictions made and tested. Captive breeding programs for ex situ conservation have borrowed and applied many of the concepts involved in welfare science to great advantage. Other keys to successful breeding programs include applying knowledge of social organization and processes to enhance reproduction; for example, finding the right combination of individuals to get animals breeding. However, behaviorists are only recently learning how to manipulate behavioral mechanisms, such as signaling behavior and mate choice, to optimize captive breeding for conservation. The emerging field of conservation behavior has played a role in captive breeding, but also is poised to play a major role in in situ conservation. Applied behavioral research can illuminate a number of issues important to conservation, including behavioral responses to habitat fragmentation and human disturbance (e.g., pollutants, noise, and light), and human–animal conflict (e.g., crop-raiding). Behavioral decisions made when animals are dispersing and selecting habitat for settlement determine the distribution of animals on the landscape and are important to understand for improving reserve and habitat corridor design. Captive–release and translocation programs require detailed behavioral knowledge to predict responses to novel environments and ensure that animals are adequately prepared for environmental change. This review underscores that many of the behavioral processes of interest to welfare science are also important for conservation behavior: perception, stress, assessment and decision-making rules, and other behavioral and physiological mechanisms. If properly understood, these mechanisms can be manipulated in the service of conservation goals, moving the field of conservation behavior from implication to application. A better integration of the disciplines of animal welfare and conservation behavior – together tackling problems at multiple levels of analysis – will further these goals.     

Tropical dry woodland loss occurs disproportionately in areas of highest conservation value

Tropical and subtropical dry woodlands are rich in biodiversity and carbon. Yet, many of these woodlands are under high deforestation pressure and remain weakly protected. Here, we assessed how deforestation dynamics relate to areas of woodland protection and to conservation priorities across the world's tropical dry woodlands. Specifically, we characterized different types of deforestation frontier from 2000 to 2020 and compared them to protected areas (PAs), Indigenous Peoples' lands and conservation areas for biodiversity, carbon and water. We found that global conservation priorities were always overrepresented in tropical dry woodlands compared to the rest of the globe (between 4% and 96% more than expected, depending on the type of conservation priority). Moreover, about 41% of all dry woodlands were characterized as deforestation frontiers, and these frontiers have been falling disproportionately in areas with important regional (i.e. tropical dry woodland) conservation assets. While deforestation frontiers were identified within all tropical dry woodland classes of woodland protection, they were lower than the average within protected areas coinciding with Indigenous Peoples' lands (23%), and within other PAs (28%). However, within PAs, deforestation frontiers have also been disproportionately affecting regional conservation assets. Many emerging deforestation frontiers were identified outside but close to PAs, highlighting a growing threat that the conserved areas of dry woodland will become isolated. Understanding how deforestation frontiers coincide with major types of current woodland protection can help target context-specific conservation policies and interventions to tropical dry woodland conservation assets (e.g. PAs in which deforestation is rampant require stronger enforcement, inactive deforestation frontiers could benefit from restoration). Our analyses also identify recurring patterns that can be used to test the transferability of governance approaches and promote learning across social–ecological contexts.     

Node self‐connections in network metrics

Zamborain‐Mason et al. (Ecol. Lett., 20, 2017, 815–831) state that they have newly proposed network metrics that account for node self‐connections. Network metrics incorporating node self‐connections, also referred to as intranode (intrapatch) connectivity, were however already proposed before and have been widely used in a variety of conservation planning applications.     

The visual definition of heritage: The restoration of domestic rural architecture in Japan 1

The paper presents an analysis of 109 restoration reports of Japanese farmhouses from the Edo period (1603–1867) that have been classified as part of the nation's architectural heritage and repaired with government funds. After reviewing farmhouse conservation in Western countries and the growth of parallel interests in Japan, the discussion focusses on the principles and practices of farmhouse restoration as documented in the reports. On this basis the paper argues that restored farmhouses often serve as status symbols for elite families of the contemporary local hierarchies and that, more generally, they constitute a visual representation of a sanitized tradition in which feudal relations and peasant existence are idealized and romanticized. Viewing farmhouse conservation as a form of visual ideology expressing dominant class interests, the paper concludes by suggesting a theoretical linkage between heritage conservation, domestic tourism, and the symbolism of nationalism.     

Abundance–occupancy patterns in a riverine fish assemblage

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Old concepts,new challenges: adapting landscape-scale conservation to the twenty-first century

Landscape-scale approaches to conservation stem largely from the classic ideas of reserve design: encouraging bigger and more sites, enhancing connectivity among sites, and improving habitat quality. Trade-offs are imposed between these four strategies by the limited resources and opportunities available for conservation programmes, including the establishment and management of protected areas, and wildlife-friendly farming and forestry. Although debate regarding trade-offs between the size, number, connectivity and quality of protected areas was prevalent in the 1970–1990s, the implications of the same trade-offs for ongoing conservation responses to threats from accelerating environmental change have rarely been addressed. Here, we reassess the implications of reserve design theory for landscape-scale conservation, and present a blueprint to help practitioners to prioritise among the four strategies. We consider the new perspectives placed on landscape-scale conservation programmes by twenty-first century pressures including climate change, invasive species and the need to marry food security with biodiversity conservation. A framework of the situations under which available theory and evidence recommend that each of the four strategies be prioritized is provided, seeking to increase the clarity required for urgent conservation decision-making.     

In vitro conservation of Dendrobium germplasm

Dendrobium is a large genus in the family Orchidaceae that exhibits vast diversity in floral characteristics, which is of considerable importance to orchid breeders, biotechnologists and collectors. Native species have high value as a result of their medicinal properties, while their hybrids are important as ornamental commodities, either as cut flowers or potted plants and are thus veritable industrial crops. Thus, preservation of Dendrobium germplasm is valuable for species conservation, breeding programs and the floriculture industry. Cryopreservation represents the only safe, efficient and cost-effective long-term storage option to facilitate the conservation of genetic resources of plant species. This review highlights 16 years of literature related to the preservation of Dendrobium germplasm and comprises the most comprehensive assessment of thorough studies performed to date, which shows reliable and reproducible results. Air-drying, encapsulation–dehydration, encapsulation–vitrification, vitrification and droplet-vitrification are the current cryopreservation methodologies that have been used to cryopreserve Dendrobium germplasm. Mature seeds, pollen, protoplasts, shoot primordia, protocorms and somatic embryos or protocorm-like bodies (PLBs) have been cryopreserved with different levels of success. Encapsulation–vitrification and encapsulation–dehydration are the most used protocol, while PLBs represent the main explant explored.     

Species richness declines and biotic homogenisation have slowed down for NW‐European pollinators and plants

Concern about biodiversity loss has led to increased public investment in conservation. Whereas there is a widespread perception that such initiatives have been unsuccessful, there are few quantitative tests of this perception. Here, we evaluate whether rates of biodiversity change have altered in recent decades in three European countries (Great Britain, Netherlands and Belgium) for plants and flower visiting insects. We compared four 20‐year periods, comparing periods of rapid land‐use intensification and natural habitat loss (1930–1990) with a period of increased conservation investment (post‐1990). We found that extensive species richness loss and biotic homogenisation occurred before 1990, whereas these negative trends became substantially less accentuated during recent decades, being partially reversed for certain taxa (e.g. bees in Great Britain and Netherlands). These results highlight the potential to maintain or even restore current species assemblages (which despite past extinctions are still of great conservation value), at least in regions where large‐scale land‐use intensification and natural habitat loss has ceased.     

Rural and Urban Students’ Perceptions of and Attitudes toward Brown Bears in Turkey

Many studies have examined adults’ perceptions of and attitudes toward large carnivores to assess human–wildlife conflict and inform conservation strategies, but there have been few studies concerning children. I studied secondary school students’ perceptions of and attitudes toward brown bears (Ursus arctos) and other large mammals in Turkey via a questionnaire survey. The questionnaire, consisting of 18 questions, was completed by 215 rural and 98 urban secondary school students. Both sets of students liked bears; they were also afraid of them and unsure about living with them in the future. While there were no gender differences in attitudes and perceptions, there were marked differences between urban and rural students. Urban students had less contact with nature, gained more of their knowledge about bears from documentaries, and had less positive attitudes toward bears. They were also more likely to be afraid of species not present in Turkey, for example, anaconda, while rural students were most afraid of wild boars. Factor analysis identified three important themes: familiarity with bears, conservation of bears, and experiencing conflict with bears, which explained 49.8% of the variance in attitudes toward bears. The most important factor for the development of negative attitudes toward bears was personal experience of human–bear conflict, suggesting that measures to reduce human–bear conflict in rural areas may help to sustain students’ positive attitudes toward the conservation of bears.     

Scale dependency of two endangered charismatic species as biodiversity surrogates

Charismatic megafauna have been used as icons and financial drivers of conservation efforts worldwide given that they are useful surrogates for biodiversity in general. However, tests of this premise have been constrained by data limitations, especially at large scales. Here we overcome this problem by combining large-scale citizen-sourced data with intensive expert observations of two endangered charismatic species, Blakiston’s fish owl (forest specialist) and the red-crowned crane (wetland specialist). We constructed large-scale maps of species richness for 52 forest and 23 grassland/wetland bird species using hierarchical community modeling and citizen-sourced data at 1, 2, 5, and 10-km grid resolutions. We compared the species richness of forest and grassland/wetland birds between the breeding and non-breeding sites of the two charismatic birds at each of the four spatial resolutions, and then assessed the scale dependency of the biodiversity surrogates. Regardless of the habitat amounts, owl and crane breeding sites had higher forest and grassland/wetland bird species richness, respectively. However, this surrogacy was more effective at finer scales (1–2-km resolutions), which corresponds to the charismatic species’ home range sizes (up to 9.4 ± 2.0 km² for fish owls, and 3–4 km² for cranes). Species richness showed the highest spatial variations at 1–2-km resolutions. We suggest that the agreement of functional scales between surrogate species and broader biodiversity is essential for successful surrogacy, and that habitat conservation and restoration targeting multiple charismatic species with different specialties can complement to biodiversity conservation.     

Structural conservation of the B subunit in the ammonia monooxygenase/particulate methane monooxygenase superfamily

The ammonia monooxygenase (AMO)/particulate methane monooxygenase (pMMO) superfamily is a diverse group of membrane‐bound enzymes of which only pMMO has been characterized on the molecular level. The pMMO active site is believed to reside in the soluble N‐terminal region of the pmoB subunit. To understand the degree of structural conservation within this superfamily, the crystal structure of the corresponding domain of an archaeal amoB subunit from Nitrosocaldus yellowstonii has been determined to 1.8 Å resolution. The structure reveals a remarkable conservation of overall fold and copper binding site location as well as several notable differences that may have implications for function and stability. Proteins 2014; 82:2263–2267. © 2014 Wiley Periodicals, Inc.     

The conservation value of elevation data accuracy and model sophistication in reserve design under sea‐level rise

Many studies have explored the value of using more sophisticated coastal impact models and higher resolution elevation data in sea‐level rise (SLR) adaptation planning. However, we know little about to what extent the improved models and data could actually lead to better conservation outcomes under SLR. This is important to know because high‐resolution data are likely to not be available in some data‐poor coastal areas in the world and running more complicated coastal impact models is relatively time‐consuming, expensive, and requires assistance by qualified experts and technicians. We address this research question in the context of identifying conservation priorities in response to SLR. Specifically, we investigated the conservation value of using more accurate light detection and ranging (Lidar)‐based digital elevation data and process‐based coastal land‐cover change models (Sea Level Affecting Marshes Model, SLAMM) to identify conservation priorities versus simple “bathtub” models based on the relatively coarse National Elevation Dataset (NED) in a coastal region of northeast Florida. We compared conservation outcomes identified by reserve design software (Zonation) using three different model dataset combinations (Bathtub–NED, Bathtub–Lidar, and SLAMM–Lidar). The comparisons show that the conservation priorities are significantly different with different combinations of coastal impact models and elevation dataset inputs. The research suggests that it is valuable to invest in more accurate coastal impact models and elevation datasets in SLR adaptive conservation planning because this model–dataset combination could improve conservation outcomes under SLR. Less accurate coastal impact models, including ones created using coarser Digital Elevation Model (DEM) data can still be useful when better data and models are not available or feasible, but results need to be appropriately assessed and communicated. A future research priority is to investigate how conservation priorities may vary among different SLR scenarios when different combinations of model‐data inputs are used.     

Land use changes and conservation threats in the eastern Selous–Niassa wildlife corridor,Nachingwea, Tanzania

Selous–Niassa miombo woodland ecosystem has been and continues to face conservation threats. Understanding of changes happening in such ecosystem overtime is important for establishing management baseline data. This study identified land use changes, socio‐economic factors and conservation threats to the Selous–Niassa wildlife corridor across Nachingwea district, Tanzania. Landsat images of 1978, 1993 and 2000 were used to assess land use changes. Household survey was conducted to obtain socio‐economic data; logistic regression model was used to analyse the data. In 15 years (1978–1993) cultivated land only increased by 131% while forestlands decreased by 8.7%. In 12 years (1993–2005) cultivated land increased by 65.6% while forestland decreased by 10.7%. Land cover change per year has been found 0.54% relatively low compared to national land cover change of 45%per year. Land tenure, shifting cultivation and crops prices were major factors influencing land use changes while wildfires, farm encroachment and illegal timber harvesting were major conservation threats. Basing on the results, it was recommended that there is a need for a government to introduce community‐based natural resource management plans to improve natural resource utilization and reduce human stress to the corridor.