Genetic diversity and structure of an endemic and critically endangered stream river salamander (Caudata: Ambystoma leorae) in Mexico

Small or isolated populations are highly susceptible to stochastic events. They are prone and vulnerable to random demographic or environmental fluctuations that could lead to extinction due to the loss of alleles through genetic drift and increased inbreeding. We studied Ambystoma leorae an endemic and critically threatened species. We analyzed the genetic diversity and structure, effective population size, presence of bottlenecks and inbreeding coefficient of 96 individuals based on nine microsatellite loci. We found high levels of genetic diversity expressed as heterozygosity (H_o = 0.804, H_e = 0.613, H_e* = 0.626 and H_Nei = 0.622). The population presents few alleles (4–9 per locus) and genotypes (3–14 per locus) compared with other mole salamanders species. We identified three genetically differentiated subpopulations with a significant level of genetic structure (F_ST = 0.021, R_ST = 0.044 y D_est = 0.010, 95 % CI). We also detected a reduction signal in population size and evidence of a genetic bottleneck (M = 0.367). The effective population size is small (Ne = 45.2), but similar to another mole salamanders with restricted distributions or with recently fragmented habitat. The inbreeding coefficient levels detected are low (F_IS = ?0.619–0.102) as is gene flow. Despite, high levels of genetic diversity A. leorae is critically endangered because it is a small isolated population.     

Combined impacts of multiple non-native mammals on two life stages of a critically endangered Neotropical tree

Despite of the widespread co-occurrence of multiple invaders, little is known on their combined ecological impacts and on their effects on different life stages of native species. We assessed the joint impacts of four non-native mammals (cattle, horse, European hare Lepus europaeus, and wild boar Sus scrofa) on seed surplus and seedling abundance of the Paraná pine (Araucaria angustifolia), a critically-endangered species of the Atlantic Forest. We found that its seeds constitute an autumn food resource for a native community richer than previously thought, with 70 bird and mammal species as confirmed or potential seed consumers, of which 40 were not previously recognized as such. We also recorded the number of uneaten seeds and seedlings at the middle-end of autumn under 520 female Paraná pine trees across the species’ distribution and identified signs of the species consuming seeds from each tree through direct observations combined with camera trapping. Most of the sampled trees (98%) were visited by at least one seed consumer species, and over 60% were visited by at least one non-native mammal. Seed surplus strongly declined in the presence of cattle, horses and wild boars, their impacts being additive, whereas the number of seedlings declined in the presence of European hares. Our results emphasize the importance of Paraná pine seeds for native fauna and the additive impact of invaders in a species-rich ecosystem. Seed predation by non-native species reduces the potential regeneration of Paraná pine forests, and may severely reduce food supply for its native consumers.     

Assessment of instream structures for habitat improvement for two critically endangered fish species

The number of fish habitat improvement schemes has greatly increased in response to the widespread degradation of aquatic ecosystems. However, many of these enhancement projects often fail to create expected habitat conditions, because they are rarely planned and executed with inputs from the species’ habitat requirements throughout their life histories, and it is frequently assumed that the implementation of a specific instream structure for habitat improvement will always benefit all species present. Using a 2D hydraulic model, the present study evaluates the potential habitat improvement for two critically endangered fish species—the Southwestern arched-mouth nase Iberochondrostoma almacai and the Arade chub Squalius aradensis—resulting from simulating the introduction of different instream structures (islands, lateral bays, and deflectors) in a modified Mediterranean river reach. The introduction of islands in the river channel was found to be the best improvement measure for YOY and juvenile nase and chub, as shown by increases in the mean annual Weighted Usable Area (WUA) of more than 100 and 50%, respectively, compared to the present conditions. On the other hand, the simulation with current deflectors proved to be the worst scenario, particularly for nase, with mean annual WUA decreasing by 3.6, 17.8 and 22.7% for YOY, juveniles and adults, respectively. The findings of this study point to the need to account for different species life-history stages when modelling the implementation of instream structures for habitat improvement and also provide a sound basis for future conservation-related studies conducted in Mediterranean rivers that harbour other threatened “sister” species.     

Development of microsatellite markers for the endangered Neotropical tree species Tibouchina papyrus (Melastomataceae)

We isolated and characterized 12 microsatellite loci for Tibouchina papyrus (Melastomataceae), an endangered species with narrow and disjunct range, endemics to a few localities in "cerrado rupestre" from Central Brazil. These microsatellites were obtained by sequencing of a genomic shotgun library for primer design. Leaves from 96 individuals collected in the three known local populations were genotyped using the 12 primers designed to analyze the polymorphisms at each locus. The number of alleles per locus ranged from one to six; two loci were monomorphic. Among the polymorphic loci, expected heterozygosities ranged from 0.161 to 0.714. Combined paternity exclusion probability was 0.957 and combined genetic identity (0.051) was high for studies on parentage. Tibouchina papyrus is a rare and endemic tree species of outcrop quartzite and sandstone soils, with highly isolated populations, which may have lead to the low degree of polymorphism that we detected. Also, motifs of most loci are larger than dinucleotide, which typically display lower levels of polymorphism.     

Comparative demographic analysis in contrasting environments of Magnolia dealbata: an endangered species from Mexico

The study of population regulation and demography in natural habitats is critical for the conservation of rare and endangered species. We address the impact of cattle exclusion on the demographics of Magnolia dealbata (Magnoliaceae), an endangered species according to IUCN and Federal Mexican laws. Sixteen permanent plots were established, eight of which were enclosed to livestock, in the mountain cloud forest in Coyopolan, Mexico, which has the largest population of M. deadlbata. Censuses of the plots were undertaken annually during three annual cycles to record seed number, recruitment, mortality, and growth (defined as length and diameter at breast height). The effects of two treatments (with and without livestock exclusion) on the dynamics of M. dealbata were investigated using transition matrix models and life table response experiment (LTRE) analysis. Contrary to expectations, there was no significant effect of cattle exclusion on population growth rates (λ). Furthermore, the λ, estimated from the mean transition matrix for both treatments was greater than one. The transitions with the highest elasticity values were similar between the two treatments, while reproductive stage contributed more to differences in population growth rate and were less variable than the non-reproductive stage. LTRE analysis showed that treatment differences had little effect on λ. Livestock exclusion appears to lead more to differences in the arrangement of the values of the transition matrix than to the rate of population growth for M. dealbata.     

A cryptic and critically endangered species revealed by mitochondrial DNA analyses: the Western Ground Parrot

We examined cytochrome b sequence data to resolve the intraspecific taxonomy of ground parrots Pezoporus wallicus. The species occurs in fragmented coastal heaths in south-eastern and south-western Australia. Net nucleotide divergences among all eastern populations were very low (0.0–0.6%) and genetic diversity unstructured, suggesting relatively recent common ancestry. Gene flow among them was probably maintained via land bridges and the persistence of suitable habitat during the Pleistocene. In contrast, net nucleotide divergence was high (4.4–5.1%) between western and eastern populations, suggesting more ancient divergence about 2 million years ago. The magnitude of divergence between eastern and western lineages is similar to a wide range of avian congeners. Our data support the need to reconsider the intraspecific taxonomy of ground parrots, and we cautiously suggest the recognition of Western Ground Parrots as a species, P. flaviventris, for conservation prioritization, planning and management purposes. Given their recent precipitous decline to approximately 110 individuals, most of which occur at one location, this makes Western Ground Parrots one of the world’s most threatened bird species.     

Two sibling species sympatrically breeding: a new conservation concern for the critically endangered Balearic shearwater

Two Puffinus shearwater species are endemic to the Mediterranean region: the Yelkouan shearwater P.␣yelkouan breeding in the central and eastern, and the critically endangered Balearic shearwater P.␣mauretanicus in the western, exclusively breeding at the Balearic archipelago. All individuals caught in Minorca, a Balearic breeding site, showed phenotypic traits of Yelkouan shearwaters. Ten birds from that colony were sampled and genetically analysed. A fragment of 857 base pairs of the cytochrome b was sequenced and compared to published sequences of both species obtained from GenBank. A Neighbor-Joining (NJ) reconstruction distinguished two clades with high bootstrap support, showing that both species bred sympatrically in that colony. This result was unexpected since shearwaters do not usually form mixed colonies. New conservation concerns arise also from our study: at first, breeding population of Yelkouan shearwaters is even smaller than previously thought; additionally, other potential threats emerge, such as hybridization and ecological competition.     

Transferability and characterization of microsatellite markers in two Neotropical Ficus species

Microsatellite markers were transferred and characterized for two Neotropical fig tree species, Ficus citrifolia and Ficus eximia. Our study demonstrated that microsatellite markers developed from different subgenera of Ficus can be transferred to related species. In the present case, 12 of the 15 primer pairs tested (80%) were successfully transferred to both of the above species. Eleven loci were polymorphic when tested across 60 F. citrifolia and 60 F. eximia individuals. For F. citrifolia, there were 4 to 15 alleles per locus, whereas expected heterozygosities ranged from 0.31 to 0.91. In the case of F. eximia, this was 2 to 12 alleles per locus and expected heterozygosities from 0.42 to 0.87.     

Commensalism facilitates gene flow in mountains: a comparison between two Rattus species

Small mammal dispersal is strongly affected by geographical barriers. However, commensal small mammals may be passively transported over large distances and strong barriers by humans (often with agricultural products). This pattern should be especially apparent in topographically complex landscapes, such as mountain ranges, where valleys and/or peaks can limit dispersal of less vagile species. We predict that commensal species would have lower genetic differentiation and higher migration rates than related non-commensals in such landscapes. We contrasted population genetic differentiation in two sympatric Rattus species (R. satarae and R. rattus) in the Western Ghats mountains in southern India. We sampled rats from villages and adjacent forests in seven locations (20–640 km apart). Capture-based statistics confirmed that R. rattus is abundant in human settlements in this region, whereas R. satarae is non-commensal and found mostly in forests. Population structure analyses using ~970-bp mitochondrial control region and 17 microsatellite loci revealed higher differentiation for the non-commensal species (R. satarae F-statistics=0.420, 0.065, R. rattus F-statistics=0.195, 0.034; mitochondrial DNA, microsatellites, respectively). Genetic clustering analyses confirm that clusters in R. satarae are more distinct and less admixed than those in R. rattus. R. satarae shows higher slope for isolation-by-distance compared with R. rattus. Although mode of migration estimates do not strongly suggest higher rates in R. rattus than in R. satarae, they indicate that migration over long distances could still be higher in R. rattus. We suggest that association with humans could drive the observed pattern of differentiation in the commensal R. rattus, consequently impacting not only their dispersal abilities, but also their evolutionary trajectories.     

Habitat suitability modelling to improve conservation status of two critically endangered endemic Afromontane forest bird species in Taita Hills,Kenya

Tropical montane forests are known to support many endemic species with restricted geographic ranges. Many of these species are however, faced with numerous threats, most notably from habitat loss and degradation, invasive alien species, and climate change. Examples include Taita Apalis and Taita Thrush. Taita Apalis (Apalis fuscigularis) and Taita Thrush (Turdus helleri) are species of birds listed as Critically Endangered by the Government of Kenya and the International Union for Conservation of Nature (IUCN). They are endemic to Taita Hills’ cloud forests in southeastern Kenya and protected under Wildlife Conservation and Management Act. As they face high risk of extinction, exploring their habitat suitability is imperative for their protection. To determine the current spatial distribution and the key ecogeographical explanatory factors and conditions affecting species distribution and indirect effects on species survival and reproduction, we employed Maximum Entropy (MaxEnt) modelling. This study was conducted in Ngangao and Vuria forests in June and July 2019 and 2020. Ngangao forest is gazetted as forest reserve and managed by the Kenya Forest Service whereas Vuria is non-gazetted and thus remains without official protection status. Ecogeographical explanatory variables; climatic, remote sensing-, LIDAR-, topography- and landscape-based variables were used in modelling and separate models were produced. 23 occurrence records of Taita Apalis and 30 of Taita Thrush from Ngangao and 21 of Taita Apalis from Vuria forests were used in the modelling. According to the models, less than 7% of the total area of Ngangao and Vuria forests was predicted as suitable habitat for Taita Apalis and Taita Thrush. This shows that these two species are more vulnerable to extinction from demographic stochasticity. Consequently, managing their habitats is critical for their long-term persistence. LIDAR-based canopy height range and elevation greatly influenced Taita Apalis distribution in Ngangao forest, with areas of high elevation (1620–1750 m a.s.l.) and having open middle-storey preferred. Elevation, slope and topographic wetness index (twi) were the major determinants of Taita Thrush distribution in Ngangao, where gentle sloping areas with moderately dry surfaces within high elevation (1620–1730 m a.s.l.) were favoured. Mean annual temperature, Euclidean distance to the forest edge, slope and land cover type greatly influenced the distribution of Taita Apalis in Vuria, with gentle sloping areas within forest interior made up of indigenous vegetation preferred. This study proposes reforesting open and degraded sites next to areas predicted as highly suitable for the two species; establishment of agroforestry belts based on indigenous trees on the boundaries of the two forests to reduce grazing and firewood collection pressure and enhance resilience to the edge effects; and enhancing forest protection through Participatory Forest Management.     

Conservation genetics of critically endangered Crepidiastrum grandicollum (Asteraceae) and two closely related woody species of the Bonin Islands,Japan

Crepidiastrum grandicollum is a critically endangered insular endemic herb found only on two oceanic islands of the Bonin Islands in Japan, namely Chichijima Island and Anijima Island. It is explicitly threatened by herbivory pressure from introduced animals. In 2009, a conservation program for C. grandicollum was begun to ensure its future persistence. To provide further information for conservation planning, we investigated the genetic diversity of C. grandicollum using 13 novel microsatellite markers in 55 individuals from four wild populations and an ex situ living collection. Two closely related woody species were also included for interspecific comparison: seven individuals of Crepidiastrum ameristophyllum and 13 of Crepidiastrum linguifolium. The 13 markers were applicable to all three species and identified 129 alleles in total. We found a clear genetic differentiation between C. grandicollum from Anijima Island and Chichijima Island. Crepidiastrum grandicollum also had low expected heterozygosity and allelic richness in populations compared to the two closely related species. Reconstructed divergence history suggested that differentiation between the islands had occurred several thousand generations ago. We suggest separate conservation units for C. grandicollum on Anijima Island and Chichijima Island given the clear (and putatively historical) genetic differentiation, which may result in speciation in the future.

     

On the edge: habitat restoration priorities for three critically endangered bird species on Sangihe,Indonesia

Remnant forests on the small Wallacean island of Sangihe north of Sulawesi hold the entire ranges of more critically endangered (CR) bird species than any other comparable area on earth. We develop habitat association models for three of these CR species to identify critical habitat features as well as areas where habitat falls slightly short of suitability, and to determine whether another area of forest away from the largest block might be suitable as an insurance site for a translocated population. Hopes for all three species appear almost totally pinned to forest within a 13 km² area of the Sahendaruman crater, with virtually no near-suitable habitat away from this site. There is, however, little overlap in habitats between one CR species and the other two: cerulean flycatcher Eutrichomyias rowleyi is associated with mature streamside forest with full canopy cover, lianas, and mid-level growth, while Sangihe whistler Coracornis sanghirensis and Sangihe golden bulbul Hypsipetes platenae are restricted to ridgetop forest with full canopy cover and large trees. We pinpoint small areas (around 5 km²) of forest in the crater that are already suitable or can be made so with habitat management, and these are absolute priorities for conservation action. We show how habitat characteristics identified within models might be enhanced, and how features, especially certain tree species, can be used as indicators of future habitat improvement.     

Heterozygote excess in ancient populations of the critically endangered Dioon caputoi (Zamiaceae,Cycadales) from central Mexico

Dioon caputoi is a long‐lived cycad known from only four populations that range in size from 50 to 120, mostly adult individuals. Dioon caputoi has the most narrow geographical range of all Dioon spp. (less than 10 km), existing completely within the boundaries of the Tehuacán–Cuicatlán Biosphere Reserve, Mexico. Negative inbreeding values were found in all four populations (F_IT = ?0.242) and within subpopulations (F_IS = ?0.379). Only c. 10% of the total genetic variation was partitioned among populations (F_ST = 0.099). We also found that most mean values of genetic variation (A = 1.91 ± 0.12; P = 78.9 ± 10.2; H_E = 0.35 ± 0.01) are within the range reported for other Dioon species with larger populations and with wider geographical ranges. These results support recent findings that rare plant species maintain high levels of genetic diversity. The heterozygote excess found at all loci is discussed in detail from a neutral evolutionary perspective, leaving arguments as working hypotheses for further research. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 158 , 436–447.     

Germination studies on three critically endangered endemic angiosperm species of the Kashmir Himalaya,India

The critically endangered and perennial alpine endemic angiosperms, namely, Aquilegia nivalis, Lagotis cashmeriana and Meconopsis latifolia inhabit such habitats in the Kashmir Himalaya that are characterised by short growing season and heavy snow cover for about 3–4 months during winter season. The seeds of these species under natural conditions experience a long period of pre-chilling during winter prior to their germination in following spring season. Taking cue from such a requirement, present study investigated the effect of chilling and exogenous application of growth hormones, NO₃ ⁻ and NH₄ ⁺ on total percent germination of otherwise deep-dormant seeds of these species, under alternate light/dark and continuous dark light regimes. Prolonged pre-chilling followed by treatment of seeds with different doses of GA₃ had a pronounced stimulatory effect on the total germination percentage in all the three species. In fact, highest germination percentage in A. nivalis was recorded only when pre-chilled seeds were treated with 1.5 mM GA₃ under alternate light/dark conditions. Likewise, germination of pre-chilled seeds of L. cashmeriana with ruptured seed coats was improved when treated with various concentrations of GA₃. Seed germination in M. latifolia was also favourably influenced by treatment of pre-chilled seeds with GA₃ or nitrogen applied either as NO₃ ⁻ or as NH₄ ⁺ under alternate light/dark conditions. Treatment of seeds with kinetin (6-furfuryl-aminopurine) had no significant influence on germination percentage in any of the three species. Thus, prolonged chilling of seeds followed by their treatment with GA₃ under alternate light/dark conditions are the requirements necessary for seed germination in these species.     

极濒危植物中华水韭屯溪居群调查研究报告

中华水韭（Isoetes sinensisPalmer）为水韭科（Isoetaceae）水韭属（Isoetes）多年生沼泽植物,由于人为干扰日益严重,现分布范围急剧缩小,种群数量稀少,处于濒危状态,已被列为国家一级重点保护野生植物。为科学合理的保护和抢救这一珍稀濒危植物资源提供理论依据,为此对中华水韭屯溪居群的生长环境、面积、株丛数量、水体的pH值、伴生植物种类和生存现状等的调查研究。中华水韭屯溪居群面积500m^2,株丛密度较大,水体pH值为6.55,伴生植物有40余种,其中10种有较高优势度,生存面临多重威胁,保护迫在眉睫。