Relic Species Research Articles

Risk of canine distemper virus vaccination of domestic dogs in giant panda habitat to giant pandas

The giant panda (Ailuropioda melanoleuca), a unique relic species in China and a global biodiversity conservation symbol, faces the threat of canine distemper virus (CDV). Vaccinating domestic dogs in panda habitats against CDV is crucial, yet the associated risks remain understudied. We investigated the safety of CDV vaccination in 69 domestic dogs within panda habitats, employing enzyme-linked immunosorbent assay for CDV antibodies and quantitative reverse transcription polymerase chain reaction for viral RNA, a marker of viral shedding. Results revealed that vaccinated dogs posed a risk through viral shedding, mainly starting from the ninth day post-vaccination. Unvaccinated dogs exhibited increased CDV antibodies and subsequent shedding, with phylogenetic analysis confirming infection from vaccinated dogs in shared kennels. Dogs with higher initial antibodies displayed reduced shedding and a markedly abbreviated shedding duration (6.7 days) than those with lower initial antibodies (9.8 days). Habitat area analysis revealed substantial overlaps between domestic dogs and wild giant pandas in two nature reserves in China. To safeguard wildlife, particularly giant pandas, we recommend restricting vaccinated dogs’ activity for at least three weeks post-vaccination, complementing existing management practices. We advocate collaborative efforts among local authorities, reserve management and villagers for effective vaccination and post-vaccination management of domestic dogs.

The current state of relic rocky grasslands with <i>Sesleria tatrae</i> and <i>Calamagrostis varia</i> in the Eastern Sudetes (Śnieżnik Massif, SW Poland)

The unique, basophilic rocky grasslands on the Pulinka rock near Kletno in the Śnieżnik Massif (Eastern Sudetes) have been known since the 1960s. The aim of the study was to, re-analyze the status of this plant community with reference to species composition, functional structure, habitat conditions and syntaxonomic position 50 years afer its discovery, and first description. For this purpose, we used archival and contemporary data. The obtained results revealed close compositional similarity between the vegetation plots collected in 1968 and 2022. The abundance of relic species documented in phytosociological relevès has remained constant (<i>Sesleria tatrae</i>, <i>Galium anisophyllon</i>) or increased (<i>Scabiosa lucida</i>). Additionally, the first locality of <i>Calamagrostis varia</i> was found on the Pulinka – a species not yet recorded in the Sudetes. On the other hand, some regular fluctuations in the abundance of sporadic species were observed. However, these were not reflected in changes in community-weighted means for environmental variables (temperature, light, nutrients, soil reaction, and moisture) and functional traits (specific leaf area, seed mass, and leaf dry matter content). We also found no differences in the functional diversity index (FD Rao) between the first and last surveys. Therefore, the lack of temporal changes in the main ecological features may indicate a high stability of the studied grasslands despite the pressure of external factors (progressive climate warming and nitrogen deposition). The phytosociological analysis carried out suggests that the studied community belongs to the class <i>Elyno-Seslerietea</i> and the order <i>Seslerietalia caeruleae</i>. However, due to the unusually poor species composition of the studied rocky grasslands, we did not find it currently possible to classify them at the alliance and association level. This requires further studies and classification based on broader data, including Western Carpathian calcicolous swards.

Insights on the fungal communities associated with needle reddening of the endangered Abies nebrodensis

AbstractAbies nebrodensis is a species of fir endemic to Sicily, represented by only 30 trees in the natural population and is currently classified as critically endangered by IUCN. In such context, monitoring its health status is essential for the proper management and preservation of this species. Phytosanitary surveys of trees of the natural population of A. nebrodensis and on potted plants raised in the local forest nursery were carried out, and the phyllosphere fungal community was investigated. The health condition of trees in the natural population were fairly good, with needle reddening and blight as the most frequently observed symptoms on the foliage, while in the nursery similar disorders were registered on about the 1.3% of potted plants. Results on fungal isolations highlighted the presence of species belonging to Valsa, Cytospora (which includes anamorphs of Valsa) and Rhizosphaera genera as the most represented on both reddened and green needles; these results suggest that these fungi likely live as endophytes, resuming their growth when needles are affected by environmental stressors such as wind, hail, mechanical wounds and do not represent a biotic constraint for A. nebrodensis. The disorders observed appear mostly as a consequence of the harsh site in which the relic species lives. Together with the fungal community observed on symptomatic and healthy needles, they indicate that A. nebrodensis adapted and tolerates its altered habitat.

First record of insects from the oldest and older Dryas of Altai (Russia). Coleoptera assemblages from Lebed River

Subfossil remains of insects found in the Lebed site (52.25220°N, 87.15692°E) located on the Lebed River, Altai Republic are recorded. The calibrated radiocarbon dates for two layers of these deposits were 16,461–17,056 cal BP, and 13,520–14,077 cal BP, which correspond to the oldest and older Dryas (Late Pleistocene). Insect assemblages of these deposits are mainly represented by Coleoptera, which are noteworthy there for high taxonomic and ecological diversity and include several endemic and relic species. At least 120 beetle species from 17 families have been found altogether, of them, 37 species are recorded for the Pleistocene deposits of Western Siberia for the first time. Three families, Carabidae, Staphylinidae and Curculionidae are most abundantly represented in the examined Lebed site. Ecologically, this beetle assemblage is dominated by species that are currently confined to the taiga belt and alpine meadows of the Altai Mountains; aquatic and near-water species are also well represented. The studied assemblages are rather different from the previously studied Pleistocene insect fauna in the south of the West Siberian Plain. The taxonomic and ecological compositions of the beetle fauna of Lebed site suggest its existence under humid palaeoclimate that was significantly colder than modern climate in this area.

Mitochondrial DNA analyses revealed distinct lineages in an alpine mammal, Siberian ibex (Capra sibirica) in Xinjiang, China.

Maternal lineages of mitochondrial DNA (mtDNA) are recognized as important components of intra and interspecific biodiversity and help us to disclose the phylogeny and divergence times of many taxa. Species of the genus Capra are canonical mountain dwellers. Among these is the Siberian ibex (Capra sibirica), which is regarded as a relic species whose intraspecific classification has been controversial so far. We collected 58 samples in Xinjiang, China, and analyzed the mtDNA genes to shed light on the intraspecific relationships of the C. sibirica populations and estimate the divergence time. Intriguingly, we found that the mtDNA sequences of C. sibirica split into two main lineages in both phylogenetic and network analyses: the Southern lineage, sister to Capra falconeri, consisting of samples from Ulugqat, Kagilik (both in Xinjiang), India, and Tajikistan; and the Northern lineage further divided into four monophyletic clades A-D corresponding to their geographic origins. Samples from Urumqi, Sawan, and Arturk formed a distinct monophyletic clade C within the Northern lineage. The genetic distance between the C. sibirica clades ranges from 3.0 to 8.6%, with values of F ST between 0.839 and 0.960, indicating notable genetic differentiation. The split of the genus Capra occurred approximately 6.75 Mya during the late Miocene. The Northern lineage diverged around 5.88 Mya, followed by the divergence of Clades A-D from 3.30 to 1.92 Mya during the late Pliocene and early Pleistocene. The radiation between the Southern lineage and C. falconeri occurred at 2.29 Mya during the early Pleistocene. Our results highlight the importance of extensive sampling when relating to genetic studies of alpine mammals and call for further genomic studies to draw definitive conclusions.

Biodiversity and genetic resources in forests of the Republic of Srpska (Bosnia and Herzegovina) – their manifold significance

The flora, fauna and fungi of Bosnia and Herzegovina are the most diverse in Europe, whereas being abundant in endemic and relic species sets this region high at the level of global biological diversity. As much as 30% of the total endemic flora of the Balkans can be found in Bosnia and Herzegovina. Negative activities in the past decreased the number and led to extinction of certain plant species, causing disruption of entire ecosystems. It is not easy to preserve and improve the use of biodiversity, particularly if forest genetic resources in the Republic of Srpska (BiH) are included. Nevertheless, if a long-term plan is made and therefore implemented, the results will be evident. Each stage of protection and breeding activities has its specific purposes and in most cases it poses only a part of the overall activities. In situ and ex situ conservation methods are applied in order to preserve the essential parts of forest communities, along with environment, populations of tree species, individual species or genes. During the last two decades, starting from quantitative and population genetics, significant progress has been made in identifying indicators of genetic diversity of species. Understanding the genetic variability of forest communities is of great importance. Without this capacity it would be impossible to achieve permanent success in preserving and conserving the gene pool of a large number of species, since understanding the genetic variability itself represents an objective parameter of intra- and interpopulation adaptive and productive potential. Previous research activites in the Republic of Srpska (BiH) at morphological level focused on comparative analyses of a larger number of quantitative and qualitative properties, moreover, at molecular level it was confirmed that tree species are abundant in genetic material, which makes the starting point for both current and future breeding processes of forest tree species. Understanding the genetic potential of forests in the Republic of Srpska (BiH), and the possibilities of its targeted use, along with the economic importance, is also crucial for the processes of forest species adaptation. It is important to keep in mind that in situ conservation objects do not represent complexes made up from forest communities which are exempted from the regime of regular management and in which cultivation and protection measures are carried outas they are usually carried in forests of special purposes, in fact, they are pilot objects which need comprehensive analyses of production, adaptive and reproductive potential of tree species population. According to multiyear analyses, it is observed that life manifestations which form the basis of population stability, in both time and space, have regime and dynamics, as well. They are essential for for complex breeding methods, such as selection and hybridization. Conservation of forest genetic resources includes extremely complex and extensive activities involving previous experience, information base and financial resources. Only a systematic approach can guarantee that all important genetic resources can be kept in reasonable number of required facilities and at acceptable costs. It should be borne in mind that there are no standard solutions for in situ and ex situ conservation. Solutions should be linked and adapted to bioecological properties of species, demographic and ecogeographic environment that prevails in conservation regions, conservation objects and within national, social and political contexts. Previous activities on forest genetic resources conservation are insufficient. Moreover, unplanned and unconscious human actions (forest exploitation, forest fires, tourism development, loss of forest land, etc.) and climate change continuously endanger genetic resources. Consequently, there is an urgent need for a comprehensive national strategy for preservation, conservation and targeted use of forest genetic resources in Bosnia and Herzegovina, which will serve as a basis for planning activities within this area.

Metabarcoding reveals seasonal and spatial patterns of arthropod community assemblages in two contrasting habitats: Desert and oasis of the Baja California Peninsula, Mexico

AbstractAimDesert springs or oases are the only permanent mesic environments in highly water‐limited arid regions. Oases have immense cultural, evolutionary and ecological importance for people and a high number of endemic and relic species. Nevertheless, they are also highly vulnerable ecosystems, with invasive species, overexploitation and climate change being the primary threats. We used the arthropod communities' spatiotemporal diversity and distribution patterns as a proxy to understand biodiversity dynamics in two geographically close but ecologically contrasting and highly threatened ecosystems: deserts and oases.LocationBaja California Peninsula, Mexico.MethodsArthropod communities at five oases and surrounding desert scrub areas were sampled in two seasons. Using DNA metabarcoding and traditional taxonomic surveys, we tried to identify what biotic and abiotic characteristics of the habitat are important drivers of arthropod diversity and how these characteristics can change across spatial and temporal scales.ResultsOver 6200 individuals representing 23 orders were collected. In oasis samples, the community composition fluctuated more in space (i.e. among sites) than in time (i.e. seasons). Thus, seasonal changes did not affect oasis community diversity and composition, but the dissimilarity among sites increased with geographic distance. Moreover, anthropic activities negatively correlated with arthropod diversity in oases. On the other hand, the season, geography (e.g. latitude) and biotic characteristics of the habitat (e.g. sampled scrub species) significantly affected the diversity and composition of the desert arthropod communities.Main ConclusionsNeutral dynamics (e.g. historical climatic events, dispersal limitation and spatial component) and human impact significantly influenced the biodiversity patterns of each oasis. In contrast, the habitat's seasonal variation and biotic characteristics were the most important variables influencing the diversity of the desert communities. Baja California oases harbour distinct invertebrate communities; therefore, each oasis should be conserved individually to preserve these unique assemblages.

Perspectives for the conservation of rare species of the genus Potentilla L. (Rosaceae) of the flora of the Republic of Bashkortostan

The article presents the results of the primary introduction experience of rare species of the genus Potentilla L. (Rosaceae Juss.) of the flora of the Republic of Bashkortostan. There are 5 rare species in the collection: the Pleistocene relic species Potentilla agrimonioides Bieb., P. arenosa (Turcz.) Juz., P. nivea L., the South Ural endemic P. eversmanniana Fisch. ex Ledeb., the Ural endemic P. kuznetzowii (Govor.) Juz. These species are included in the Red Data Book of the Republic of Bashkortostan (2021). In the collection, each species is represented by one sample. The mobilization was carried out by seeds from natural populations. Species of the genus Potentilla were grown in monoculture in the introduction nursery of the Ufa Institute of Biology. Plants go through a full cycle of annual development of shoots and give viable seeds (except P. arenosa). According to the scale of introduction resistance proposed by N.V. Trulevich (1991), under cultivation in the forest-steppe zone of the republic, P. agrimonioides and P. kuznetzowii are resistant species, P. eversmanniana and P. nivea are weakly resistant, P. arenosa is unstable species.

Transformations of Vascular Flora of a Medieval Settlement Site: A Case Study of a Fortified Settlement in Giecz (Wielkopolska Region, Western Poland)

Exceptional components of the cultural landscape of Central Europe include archaeological sites, e.g., castle ruins, prehistoric or medieval fortified settlements, other settlements and burial mounds. The plants associated with them help us explain the processes of species persistence on habitat islands as well as the process of naturalization of crop species, which escape from fields or are abandoned. This study describes the flora of a medieval fortified settlement in Giecz (Wielkopolska region, western Poland), presents plant indicators of former settlements (relics of cultivation), species of high conservation value, and transformations of the vascular flora of this settlement over a few decades. Field research was conducted in 1993–1994, 1998–1999, and 2019. At the study site, 298 species of vascular plant species were recorded, and nearly 70% of them (201 species) have persisted there over the last 20 years. The flora includes seven relics of cultivation (Artemisia absinthium, Leonurus cardiaca, Lycium barbarum, Malva alcea, Pastinaca sativa, Saponaria officinalis, and Viola odorata), 5 species threatened with extinction in Poland and/or Wielkopolska, and 53 species of least concern (LC) according to the European red list. We have attempted to explain the floristic changes. The archaeological site in Giecz is of high conservation value, very distinct from the surrounding cultural landscape because of its specific flora, and composed of species from various habitats (e.g., dry grasslands, wooded patches, meadows, aquatic and ruderal habitats), including threatened, protected, and relic species.

Effects of Household Resource Utilization Behaviors on Giant Panda Habitat under the Background of Aging: Evidence from Sichuan Province.

The Giant Panda (Ailuropoda melanoleuca) is a flagship species for endangered wildlife conservation and is a specific relic species in China. Its habitat conservation has received widespread attention around the world. Since 2010, the phenomenon of an aging labor force gradually appeared within the Giant Panda Nature Reserve and its surrounding communities. Under the new labor force structure, households' resource utilization behavior has had different characteristics, which has led an evolution in giant panda habitats. This study is based on a questionnaire and geographic data. It reveals the internal mechanisms of households' resource utilization behavior impacting giant panda habitat patterns under the ongoing trend of labor force aging. The study shows that labor force aging has promoted rising ecological niche widths and falling ecological niche overlaps. These could drive a growth in giant panda habitat globally. From a spatial perspective, nature reserves with lower comprehensive ecological niche widths and higher ecological niche overlaps face greater conflict between conservation and development. However, the phenomenon of labor force aging mitigates these ecological conflicts to a certain extent.

Analysis of the enzyme activity of the Rubus chamaemorus L. antioxidant system

Currently, biodiversity conservation is one of the key areas for sustainable development of the world economy. A combination of abiotic and biotic factors constantly affects the plant community. Often, together with anthropogenic stress factors, they adversely affect the ability of plants to adapt without compromising physiological parameters and to narrow the limits of tolerance and resistance. One of the options for determining the susceptibility or resistance of populations to climatic conditions and anthropogenic stress factors is to study the complex of enzymes responsible for the formation of the antioxidant defense of the cell. Cloudberry squat refers to relict plants that are endangered in the Republic of Belarus.The studies have shown that the most oppressed of the studied populations of Rubus chamaemorus L. is “Zhada”; however, ongoing measures to restore the hydrological regime of this territory can have a positive impact on its future condition. These studies were carried out for the first time for the southern border of the habitat.“Lonno” population plants are assessed as the most promising ones for use in breeding and distribution of cloudberries that, in turn, will allow preserving this relic species in Belarus.

Quantifying the Evolution of Giant Panda Habitats in Sichuan Province under Different Scenarios

The giant panda (Ailuropoda melanoleuca) is a relic species in China and a flagship species in the field of endangered wildlife conservation. The conservation of the giant panda’s habitat has gained widespread attention for this reason. Historically, Chinese Giant Panda Nature Reserves are surrounded by communities and the resource utilization behavior of households disturbs the giant panda habitat. Changes in these communities and in Giant Panda Nature Reserves began around 2010, with the feminization and aging of the farm labor force. These changes brought different resource utilization behaviors that led to different evolutionary tendencies in giant panda habitats. This research study assesses the impact of these tendencies based on data from the fourth survey of the giant panda in the Sichuan Province and from geographic information data. The paper aims to uncover the internal mechanisms of farmers’ resource utilization behavior in terms of the changes wrought to giant panda habitats. The paper simulates the future habitat of the giant panda based on the LUCC (land use/cover change) model to identify anticipated changes in future landscape patterns and the habitat quality of giant pandas under the current scenarios. The paper analyzes the spatial-temporal change of landscape patterns through the land use transfer matrix, based on the Markov model. The results of the scenario analyses illustrate the spatial and temporal difference in habitat quality. The driving mechanism for landscape pattern change is explored using the logistic regression model. The paper simulates the variation tendency of giant panda habitats under differential labor force structures and resource utilization behavior based on the CA (cellular automata) model, with the robustness of the results verified by participatory experiment. Through four scenarios of simulated farm labor force structure and resource utilization behavior, results suggest that the quality of giant panda habitats in the future will be relatively high when workforce feminization and aging is intense and resource utilization behavior is weakened. The simulated results confirm that the current agricultural labor force structure can reduce the intensity of resource utilization behavior. In this scenario, disturbance to giant panda habitats would decrease and their quality would improve.

Concealing Dirac neutrinos from cosmic microwave background

The existence of prolonged radiation domination prior to the Big Bang Nucleosynthesis (BBN), starting just after the inflationary epoch, is not yet established unanimously. If instead, the universe undergoes a non-standard cosmological phase, it will alter the Hubble expansion rate significantly and may also generate substantial entropy through non-adiabatic evolution. This leads to a thumping impact on the properties of relic species decoupled from the thermal bath before the revival of the standard radiation domination in the vicinity of the BBN. In this work, considering the Dirac nature of neutrinos, we have studied decoupling of ultra-relativistic right-handed neutrinos (νR s) in presence of two possible non-standard cosmological phases. While in both cases we have modified Hubble parameters causing faster expansions in the early universe, one of the situations predicts a non-adiabatic evolution and thereby a slower redshift of the photon temperature due to the expansion. Considering the most general form of the collision term with Fermi-Dirac distribution and Pauli blocking factors, we have solved the Boltzmann equation numerically to obtain ΔNeff for the three right-handed neutrinos. We have found that for a large portion of parameter space, the combined effect of early decoupling of νR as well as the slower redshift of photon bath can easily hide the signature of right-handed neutrinos, in spite of precise measurement of ΔNeff, at the next generation CMB experiments like CMB-S4, SPT-3G etc. This however will not be applicable for the scenarios with only fast expansion.

Deeply divergent freshwater fish species within a single river system in central Sulawesi

Sulawesi is a biodiversity hotspot for ricefishes (Adrianichthyidae), with many species endemic to the central part of this island in single ancient lakes or lake systems. Frequent vicariance by lake fragmentation since the Pliocene may be largely responsible for diversification in this family. In this study, we demonstrate that not only lacustrine species but also riverine species in this area are also deeply divergent even within a single river system. A mitochondrial phylogeny revealed that a ricefish population newly discovered from Cerekang River is sister to Oryzias dopingdopingensis Mandagi, Mokodongan, Tanaka, & Yamahira, another riverine species endemic to Doping-doping River. However, the Cerekang Oryzias was genetically isolated from O. dopingdopingensis, despite that Cerekang River and Doping-doping River share a connection across estuarine waters. This separation was supported by phylogenomic trees and population genetic structure analyses based on genome-wide single nucleotide polymorphisms. Coalescent-based demographic inference demonstrated that the ancestral population of these two riverine ricefishes had experienced a substantial population decrease and subsequently diverged into two sub-populations. Because the Cerekang Oryzias was also morphologically distinguished from O. dopingdopingensis, we described it as a new species, O. landangiensis. We infer that O. landangiensis and O. dopingdopingensis are of lake-origin and are relic species which were left in these rivers after the lake disappeared, and that they have lost their dispersal ability when inhabiting the ancient lake. The lost dispersal ability possibly contributed to the formation of the biodiversity hotspot for this fish group on this island.

Full-sky, Arcminute-scale, 3D Models of Galactic Microwave Foreground Dust Emission Based on Filaments

Abstract We present the DustFilaments code, a full-sky model for the millimeter Galactic emission of thermal dust. Our model, composed of millions of filaments that are imperfectly aligned with the magnetic field, is able to reproduce the main features of the dust angular power spectra at 353 GHz as measured by the Planck mission. Our model is made up of a population of filaments with sizes following a Pareto distribution ∝ L a − 2.445 , with an axis ratio between short and long semiaxes ϵ ∼ 0.16 and an angle of magnetic field misalignment with a dispersion rms(θ LH) = 10°. On large scales, our model follows a Planck-based template. On small scales, our model produces spectra that behave like power laws up to ℓ ∼ 4000 or smaller scales by considering even smaller filaments, limited only by computing power. We can produce any number of Monte Carlo realizations of small-scale Galactic dust. Our model will allow tests of how the small-scale non-Gaussianity affects CMB weak lensing and the consequences for the measurement of primordial gravitational waves or relativistic light relic species. Our model also can generate frequency decorrelation on the modified blackbody spectrum of dust and is freely adjustable to different levels of decorrelation. This can be used to test the performance of component separation methods and the impact of frequency spectrum residuals on primordial B-mode surveys. The filament density we paint in the sky is also able to reproduce the general level of non-Gaussianities measured by Minkowski functionals in the Planck 353 GHz channel map.

Ancient introgression underlying the unusual mito‐nuclear discordance and coat phenotypic variation in the Moupin pika

AbstractAimThe mechanisms by which global biodiversity hotspots harbour and conserve high genetic and morphological diversity of endemic species remain unexplored. Relic species of ochotonids in the genus Ochotona are confined to alpine habitats and highly sensitive to environmental changes. We studied the genomic and ecological mechanisms underlying the divergence and adaptive evolution of the Moupin pika (O. thibetana) and its closely related species to infer its diversification, adaptive evolution and demographic history in response to historical and recent environmental changes.LocationHengduan Mountain Region, China.MethodsWe integrated morphological, genomic and ecological data to interpret the phylogeographic structure, adaptive evolution, demographic history and range shift of O. thibetana. Phylogenetic reconstruction was based on Cytochrome b (CYTB), the mitochondrial genome and single‐copy orthologues of the whole genome. Gene flow among extant lineages, as well as from extinct species, was inferred by multiple algorithms. Demographic history was inferred using the pairwise sequential Markovian coalescent and high‐resolution analysis of linkage disequilibrium. We also predicted the range shift of this species by using ecological niche modelling.ResultsPhylogenetic reconstruction revealed an unusual mitochondrial lineage of O. thibetana from the western Sichuan Basin, which was named O. qionglaiensis in previous studies. Extensive gene flow was detected among genetic lineages of O. thibetana, which has distinct phenotypic variation in hair thickness and colouration, as well as notable morphological differentiation in external and craniodental measurements. Multiple members of the keratin gene family were identified as introgressed loci from some ancient species to O. thibetana. The Moupin pika underwent dramatic population shrinkage in the late Quaternary, with a clear trend of population growth in approximately the last 70 generations. The potential distribution range of O. thibetana showed a clear trend of expansion in the future.Main conclusionsThe unusual mitochondrial phylogenetic pattern of O. thibetana resulted from “extended ghost introgression,” a new evolutionary model proposed in the present study, and thus rejected the validity of O. qionglaiensis as an independent species. Ancient introgression of keratin genes likely underlies the prominent coat phenotypic variation among genetic lineages. Clear population growth and range expansion of the Moupin pika in recent generations probably benefitted from recent global warming and vegetation recovery, which not only contributed to the conservation of large mammals but was also beneficial to small mammals endemic to alpine habitats.

The genome of the Paleogene relic tree Bretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs.

Among relic species, genomic information may provide the key to inferring their long-term survival. Therefore, in this study, we investigated the genome of the Paleogene relic tree species, Bretschneidera sinensis, which is a rare endemic species within southeastern Asia. Specifically, we assembled a high-quality genome for B. sinensis using PacBio high-fidelity and high-throughput chromosome conformation capture reads and annotated it with long and short RNA sequencing reads. Using the genome, we then detected a trade-off between active and passive disease defences among the gene families. Gene families involved in salicylic acid and MAPK signalling pathways expanded as active defence mechanisms against disease, but families involved in terpene synthase activity as passive defences contracted. When inferring the long evolutionary history of B. sinensis, we detected population declines corresponding to historical climate change around the Eocene–Oligocene transition and to climatic fluctuations in the Quaternary. Additionally, based on this genome, we identified 388 single nucleotide polymorphisms (SNPs) that were likely under selection, and showed diverse functions in growth and stress responses. Among them, we further found 41 climate-associated SNPs. The genome of B. sinensis and the SNP dataset will be important resources for understanding extinction/diversification processes using comparative genomics in different lineages.

Juniperus excelsa s. str. in crimea – differentiation and history inferred from genetic and morphological markers

Abstract Juniperus excelsa s. str. (Greek juniper) in Crimea is a relic species on the limits of its range, and represents the Mediterranean flora in the Sub-Mediterranean part of the peninsula. Its origin and history in this area remains unresolved. We aimed to analyze phylogeny and potential demographic expansion of the juniper in the Crimea as well as to study its morphological differentiation. We analyzed plant material from 59 trees inhabiting eight populations. Genetic variation assessments were based on the four non-coding chloroplast DNA (cpDNA) fragments and the nuclear internal transcribed spacer region ITS1-5,8S-ITS2 (ITS). To examine the morphological differentiation, eight measured/counted traits of cones, seeds, and shoots were chosen and eight ratios were calculated. Morphological parameters were compared using ANOVA, Student’s t test, discrimination analysis and Kruskal-Wallis and U Mann-Whitney tests. Two cpDNA fragments were polymorphic and, in total, 10 cpDNA haplotypes were found. Haplotype diversity (Hd) ranged from 0.0 to 0.9. Based on both cpDNA and ITS sequences variation, phylogenetic analyses revealed a close relationship of the Crimean junipers to the individuals from other parts of the species range. In general, our molecular results confirmed the low level of genetic differentiation of J. excelsa individuals inhabiting different parts of the species range, likely resulting from a common ancestry. Only slight morphological differences were found between populations with different geographic location or habitat. The analyzes showed the distinctness of the populations from the southern part of the coast. Some unique morphological and molecular features of southern coastal populations imply that they are remnants of Late Pleistocene abundant forests. We suggest that the recent fragmentation of the Juniperus populations in the Crimean Peninsula could have arisen during the Atlantic period of the Holocene.

Neogene long-term trends in climate of the Colchic vegetation refuge in Western Georgia – Uplift versus global cooling

West Georgia is part of the Caucasus biodiversity hotspot and hosts the Colchic vegetation, a ‘Tertiary’ refuge, with many endemic and relic species. Based on fossil pollen records from 21 localities in west Georgia quantitative climate reconstruction has been carried out covering the Miocene, Pliocene, and Pleistocene periods. Further, major shifts in vegetation have been unraveled using the biomization procedure. The obtained results were compared to global climate patterns and generally matched the late Neogene cooling trend as well as the subsequent cooling during the Pleistocene. However, the decrease in temperature in west Georgia was not accompanied by an increase in seasonality during the Mio- and Pliocene and no significant decrease in precipitation was observed. Climate stayed overall humid and mean annual temperatures never dropped significantly beneath modern values. These findings show that regional influences, like the buffering effect of the presence of the Paratethys and its remnants, modulated the climate in west Georgia. Even more importantly, since the Early Pleistocene the uplift of the Caucasus mountain range counteracts global climatic changes. This unique interplay of global climate and regional tectonic effects led to favorable climatic conditions for the development of the Colchic vegetation refuge.

Prunus lusitanica L.: An Endangered Plant Species Relict in the Central Region of Mainland Portugal

Prunus lusitanica L. is a paleotropical relic species with an Ibero-Maghrebian distribution, which is presently considered as an endangered species, recognized by the Natura 2000 Network (92/43/EEC) as a priority habitat for conservation in Europe. The mountains in the Portuguese mainland central region offer the best location for this species to occur. The main objective of this study is to measure the current conservation status of the communities of P. lusitanica, through the collection of field data, such as the number of existing individuals of each population and their location, which will then be comparatively analyzed based on the previous literature, published at least 15 years ago. Soil characterization analysis was carried out and the main threats to conservation were identified. As a result, a decline of approximately 40% was observed in the number of individuals and in the quality of their habitat. The main threats to their conservation were found to be the seasonal occurrence of rural fires and the expansion of invasive species, such as Acacia dealbata Link and Ailanthus altissima (Mill.) Swingle. Finally, we present the main management methodologies that should be considered for the valorization of this important vegetational relic in the central region of mainland Portugal.