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PubMed2005

New species of woolly lemur Avahi (primates: lemuriformes) in Bemaraha (Central Western Madagascar).

There are at least three distinct taxa of woolly lemurs (genus Avahi) in western Madagascar. The range of Avahi occidentalis extends north and east of the Betsiboka River to the Bay of Narinda. Avahi unicolor occurs well to the north, including the Ampasindava peninsula and the Manongarivo Special Reserve. Here we describe a third Avahi population in central western Madagascar, which was discovered in the Bemaraha Strict Nature Reserve in the Tsingy de Bemaraha region, north of the Manambolo River. The description is based on a released type individual from which we obtained hair samples, photographs, and tape and video recordings. Its entire range is believed to be less than 5,000 km(2), and forest loss, along with an observed continuing decline in numbers, indicates that this species should be considered Endangered or even Critically Endangered, according to the Red List criteria of the World Conservation Union-IUCN.

Animals↗

PubMed2005

Is the chimpanzee, Pan troglodytes, an endangered species? It depends on what "endangered" means.

I review information on the status in the wild of the robust chimpanzee, Pan troglodytes, and consider whether this evidence is consistent with the designation of P. troglodytes as Endangered in the International Union for the Conservation of Nature and Natural Resources (IUCN) Red List, and with public statements to the effect that great apes as a whole will be extinct within a few decades. Chimpanzees remain widespread in tropical Africa, occurring in a variety of forested habitats. Estimates of total surviving numbers have increased from about 200,000 in the 1980s to a maximum of almost 300,000 in 2003. However, this apparent increase comes about from new survey data, rather than representing a measured increase in actual population numbers. Infectious disease decimated several chimpanzee populations during the 1990s, and data from parts of Gabon, extrapolated to that country as a whole, suggest a major decline in great ape populations caused by disease and hunting. However, accurate data on population numbers are absent for the majority of wild chimpanzee populations. I found reports of the presence of Pan troglodytes in at least 51 national parks in at least 19 countries; some of these parks have been established very recently. Chimpanzees also occur in many non-park conservation areas. A set of large, well-protected parks could safeguard chimpanzees for the foreseeable future. Although many African parks do not function well at present, mechanisms to improve their function are understood and available. By a strict application of IUCN threat criteria, P. troglodytes can be considered Endangered, based on estimated rates of past decline and on the species' long generation time. Relatively speaking, however, P. troglodytes is less endangered than are orangutans or gorillas, and the species is unlikely to go extinct by the year 2100, especially if existing conservation measures improve. The IUCN threat-rating system has become overly complex; the system can produce results that do not accord with common sense and these results must therefore be interpreted with care.

Africa↗

PubMed2006

Phylogeny and biogeography of ice crawlers (Insecta: Grylloblattodea) based on six molecular loci: designating conservation status for Grylloblattodea species.

Ice crawlers (Insecta: Grylloblattodea) are rarely encountered insects that consist of five genera representing 26 species from North America and Asia. Asian grylloblattids are the most diverse, but North American ice crawlers (genus Grylloblatta) are known for their adaptation to cold conditions. Phylogenetic relationships among grylloblattid species and genera are not known. Six genes were sampled in 35 individuals for 18S rRNA, 28S rRNA, histone 3, 12S rRNA, 16S rRNA, and cytochrome oxidase II from 21 populations of Grylloblatta, three populations from Japan (genus Galloisiana), and three populations from Russia (genus Grylloblattina). Phylogenetic analysis of these data with two mantophasmid outgroups in POY supported monophyletic genera, with Grylloblatta as sister to Grylloblattina. Grylloblatta was shown to contain two major lineages: a clade in Northern California and Oregon and a clade in Washington and Oregon. One new species and six candidate species are proposed. IUCN Red List Conservation Criteria were implemented to designate conservation status for each lineage.

Animals↗

PubMed2026

The overlooked conservation values of saline lakes.

Saline lakes are hypersensitive to changes in their water balance and therefore show amplified responses to climatic and land-use changes in their catchment. Despite often dramatic ecological impacts, saline lakes rank low on policy agendas as they are assumed to support few ecosystem services and low levels of biodiversity. Here, we challenge this view and evaluate ecosystem services and threatened species in 85 saline lakes distributed across the globe. We show that saline lakes support, additionally to threatened aquatic biota, a diverse range of red-listed terrestrial species that contribute together with a large beta diversity to their conservation value. Further, our results highlight that saline lakes provide a number of culturally and economically important ecosystem services but several of them are 'hidden' and difficult to quantify. We conclude our analysis with best-practice recommendations for sustainable management of saline lakes. Their local adaptation and implementation will be key for safeguarding biodiversity and ecosystem services of these valuable and highly sensitive ecosystems.

Lakes↗

PubMed2025

Chromosome-level genome assembly of the Vermilion Snapper (Rhomboplites aurorubens).

Vermilion Snapper (Rhomboplites aurorubens, Lutjanidae) inhabits deep waters (20-300 m) from North America to Brazil and supports significant commercial and recreational fisheries. Despite its economic importance, the understanding of its basic biology remains limited. Classified as Vulnerable on the Red List due to overfishing, populations have declined by over 30% in recent generations. We assembled and annotated the first chromosome-scale genome of this species by combining PacBio long reads, Illumina short reads, and Hi-C data. The resulting assembly is 987.5 Mbp, with a scaffold N50 size of 41.3 Mbp, and includes 135 contigs clustered and ordered onto 24 chromosomes with 34,496 predicted genes. The high-quality assembly and annotation contained about 98% complete and single-copy BUSCO genes. It is the most complete, chromosome-level genome assembly of an Atlantic snapper to date. The genome assembly and supporting data are valuable tools for ecological and comparative genomics studies of snappers and other valuable commercial species within the family.

Chromosomes↗

PubMed1997

Analysis of population genetic structure and variability using RAPD markers in the endemic and endangered Limonium dufourii (Plumbaginaceae).

Limonium dufourii (Plumbaginaceae) is a triploid species, with apomictic reproduction, endemic to the east mediterranean coast of Spain, where it is present in only six populations with a few individuals in most of them. L. dufourii is included in the Red List of Endangered Species by the IUCN. Genetic variation and population structure in this species has been studied using RAPDs. Twelve different primers provided 124 reliable bands of which 33 were polymorphic among the 165 individuals analysed. Those polymorphic bands were able to define 44 different patterns, of which all but six were present in only one population. Several methods for statistical evaluation have been used for intra- and interpopulation analysis of genetic variability. Relationships among patterns have led to the identification of four main clusters. Two of them show a perfect correspondence to the population of origin of those individuals that present them (Cullera and Torreblanca), and the other two (Groups A and B) include patterns found in individuals coexisting in the same populations (Marjal del Moro populations) and in El Saler. Most of the variation found in this species is due to differences among populations as shown by the analysis of molecular variance. This agrees with the expectation for an apomictic species such as L. dufourii. The analysis of homogeneity of variance shows that substantial differences in the amount of genetic variability present in the six populations exist. These results have been used to understand the evolutionary and demographic history of L. dufourii, which is a requisite in order to establish efficient conservation measures for this species.

DNA Primers↗

PubMedDate not supplied

Selection of relevant non-target herbivores for monitoring the environmental effects of Bt maize pollen.

Genes of Bacillus thuringiensis var. kurstaki (Berliner) that encode lepidopteran-specific toxins were engineered into maize for protection against the European Corn Borer, Ostrinia nubilalis (Hbn.). Recent data suggest that Lepidoptera may be negatively affected, if maize pollen contains high amounts of Bt toxin and is diposited on host plants near maize fields. Monitoring the environmental effects of commercial Bt maize fields requires effective use of limited financial and logistical resources. The aim of this study was to develop and apply tools for selecting relevant herbivore species for the field monitoring of environmental Bt toxin effects via pollen deposition. We first present a theoretical selection tree based on "risk index of Bt pollen for herbivores" (I(Btp)). Our index consists of five classes from zero (not relevant) to four (highly relevant) derived from data on potential temporal and spatial coincidence of pollen exposure (A), feeding mode (B), susceptibility to lepidopteran-specific Bt toxins (C) and hazard to rare and/or endangered species ("Red List") (D). We then screened the Macrolepidoptera database LEPIDAT to identify relevant species in Germany. Finally, we also applied the index to species found in a local biocoenotic field study (Bonn, Western Rhineland, Germany). Approximately 7% of the German Macrolepidoptera species mainly occur in farmland areas and were selected as being potentially affected by Bt pollen exposure. Of these species, 14% (= 1% of total) were found to be potentially exposed on a regional scale. The combination of I(Btp) and database screening enables us to pre-select species for monitoring purposes.

Animals↗

PubMed2005

Climate change threats to plant diversity in Europe.

Climate change has already triggered species distribution shifts in many parts of the world. Increasing impacts are expected for the future, yet few studies have aimed for a general understanding of the regional basis for species vulnerability. We projected late 21st century distributions for 1,350 European plants species under seven climate change scenarios. Application of the International Union for Conservation of Nature and Natural Resources Red List criteria to our projections shows that many European plant species could become severely threatened. More than half of the species we studied could be vulnerable or threatened by 2080. Expected species loss and turnover per pixel proved to be highly variable across scenarios (27-42% and 45-63% respectively, averaged over Europe) and across regions (2.5-86% and 17-86%, averaged over scenarios). Modeled species loss and turnover were found to depend strongly on the degree of change in just two climate variables describing temperature and moisture conditions. Despite the coarse scale of the analysis, species from mountains could be seen to be disproportionably sensitive to climate change (approximately 60% species loss). The boreal region was projected to lose few species, although gaining many others from immigration. The greatest changes are expected in the transition between the Mediterranean and Euro-Siberian regions. We found that risks of extinction for European plants may be large, even in moderate scenarios of climate change and despite inter-model variability.

Biodiversity↗

PubMed2005

Allozyme variation in the three extant populations of the narrowly endemic cycad Dioon angustifolium Miq. (Zamiaceae) from North-eastern Mexico.

BACKGROUND AND AIMS: Dioon angustifolium was considered within D. edule. Recent morphometric and allozyme studies on D. edule have shown that D. angustifolium has originated from geographic isolation and is therefore considered to be a separate species. This cycad is endemic to north-eastern Mexico and is known only from three populations in the Sierra Madre Oriental mountain chain. Its populations are small when compared with its southern relative D. edule. In this study, genetic variation was determined within and between populations of D. angustifolium and the genetic consequences of habitat fragmentation and isolation of populations of this species were assessed. METHODS: Allozyme electrophoresis of 14 presumptive loci was used. The data were analysed with statistical approximations for estimating genetic diversity, structure, gene flow and recent genetic bottlenecks. KEY RESULTS: Means and standard deviations of genetic diversity estimators were: number of alleles per locus (A = 1.67 +/- 0.23), percentage of polymorphic loci (P = 52.4 +/- 23 %) and expected heterozygosity (H(E) = 0.218 +/- 0.093). The genetic variation attributable to differences among populations was 16.7 %. Mean gene flow between paired populations was Nm = 1.55 +/- 0.67, which is similar to that reported for endemic plant species of narrow geographical distribution and species with gravity-dispersed seed. A recent bottleneck is detected in the populations studied. CONCLUSIONS: Dioon angustifolium presents high levels of genetic diversity compared with other cycad species, in spite of small population sizes. The recent bottleneck effect did not effectively reduce the genetic variation to the extent of eliminating these populations. The distribution of D. angustifolium appears to be the result of historical biogeographical effects related to the Pleistocene glaciations. It is recommended that this species be catalogued in the IUCN Red List of Threatened Species and conservation efforts be made to preserve it.

Climate↗

PubMed2026

Genomic erosion in the assessment of species' extinction risk and recovery potential.

Many species are undergoing rapid population declines and environmental deterioration, leading to genomic erosion. Here we define genomic erosion as the loss of genetic diversity, accumulation of deleterious mutations, maladaptation, and introgression, all of which can undermine individual fitness and long-term population viability. Critically, this process continues even after demographic recovery due to a time-lagged impact of genetic drift, which is known as drift debt. Current conservation assessments, such as the International Union for Conservation of Nature Red List, focus on short-term extinction risk and do not capture the long-term consequences of genomic erosion. Likewise, the longer-term assessments of the International Union for Conservation of Nature Green Status may overestimate population recovery by failing to account for the enduring effects of genomic erosion. As genome sequencing becomes increasingly accessible, there is a growing opportunity to quantify genomic erosion and integrate it into conservation planning. Here, we use genomic simulations to illustrate how different genomic metrics are sensitive to the drift debt. We test how ancestral effective population size (Ne) and bottleneck history influence the tempo and severity of genomic erosion. Furthermore, we demonstrate how these dynamics shape genetic load and additive genetic variation, which are key indicators of long-term evolutionary potential. Finally, we present a proof-of-concept for a Genomic Green Status framework that aligns genomic metrics with conservation impact assessments, laying the foundation for genomics-informed strategies to support species recovery.

Extinction, Biological↗

PubMed2006

Mass-dependent predation risk as a mechanism for house sparrow declines?

House sparrow (Passer domesticus) numbers have declined rapidly in both rural and urban habitats across Western Europe over the last 30 years, leading to their inclusion on the UK conservation red list. The decline in farmland has been linked to a reduction in winter survival caused by reduced food supply. This reduction in food supply is associated with agricultural intensification that has led to the loss of seed-rich winter stubble and access to spilt grain. However, urban house sparrows have also declined, suggesting that reduced food supply in farmland is not the sole reason for the decline. Here, we show that changes in house sparrow mass and thus fat reserves are not regulated to minimize starvation risk, as would be expected if limited winter food were the only cause of population decline. Instead, the species appears to be responding to mass-dependent predation risk, with starvation risk and predation risk traded-off such that house sparrows may be particularly vulnerable to environmental change that reduces the predictability of the food supply.

Animals↗

PubMed2025

Large future genetic diversity losses are predicted even with habitat protection.

Genetic diversity within species is the basis for evolutionary adaptive capacity and has recently been included as a target for protection in the United Nations' Global Biodiversity Framework (GBF). However, we lack large-scale mathematical frameworks to quantify how much genetic diversity has already been lost, let alone to predict future losses under 21st century conservation scenarios. To fill this gap, we developed an area-based spatio-temporal predictive framework of genetic diversity calibrated with population-scale genomic data of 29 plant and animal species. To estimate present genetic diversity loss with our framework, we used species' habitat area and population sizes losses reported in the Living Planet Index, the Red List, and new GBF indicators across 13,808 species for the last 5 decades. Applying our evolutionary framework across these species, we estimate genetic diversity loss lags behind population and habitat area declines, with an estimated current 13-22% π genetic diversity loss. However, we forecast future genetic diversity losses will reach 41-76% even if populations are not further contracted. These results highlight that safeguarding existing habitats is insufficient to maintain the genetic health of species and relying solely on continuous genetic monitoring underestimates lagging long term impacts.

Genetic diversity↗

PubMed2001

Ecological risk-benefit analysis of a wetland development based on risk assessment using "expected loss of biodiversity".

Ecological risk from the development of a wetland is assessed quantitatively by means of a new risk measure, expected loss of biodiversity (ELB). ELB is defined as the weighted sum of the increments in the probabilities of extinction of the species living in the wetland due to its loss. The weighting for a particular species is calculated according to the length of the branch on the phylogenetic tree that will be lost if the species becomes extinct. The length of the branch on the phylogenetic tree is regarded as reflecting the extent of contribution of the species to the taxonomic diversity of the world of living things. The increments in the probabilities of extinction are calculated by a simulation used for making the Red List for vascular plants in Japan. The resulting ELB for the loss of Nakaikemi wetland is 9,200 years. This result is combined with the economic costs for conservation of the wetland to produce a value for the indicator of the "cost per unit of biodiversity saved." Depending on the scenario, the value is 13,000 yen per year-ELB or 110,000 to 420,000 yen per year-ELB (1 US dollar = 110 yen in 1999).

Ecology↗

PubMed2005

On the verge of extinction: genetics of the critically endangered Iberian plant species, Borderea chouardii (Dioscoreaceae) and implications for conservation management.

Borderea chouardii is a relictual and dioecious, strictly sexually reproducing, long-living geophyte of the Dioscoreaceae family. Previous biological and demographic studies have indicated the existence of a uniformly distributed panmictic population of this taxon at the southernmost Spanish pre-Pyrenean mountain ranges where it occurs in rather inaccessible crevices of a single limestone cliff. However, individuals of B. chouardii are spatially subdivided into two subpopulations located, respectively, on the upper and lower parts of the cliff, and vertically separated 150 m. Because of its extreme rarity, B. chouardii was the first Iberian taxon to have a specific conservation plan and has been included in several red lists under the category of critically endangered (CR). However, no previous attempts have been conducted to analyse the fine scale evolutionary mechanisms involved in its present microspatial distribution. Genetic diversity and population structure have been investigated through the analysis of neutral hypervariable markers such as simple sequence repeats (SSRs) and randomly amplified polymorphic DNAs (RAPDs) to unravel the impact of life history traits in the differentiation of the two subpopulations. Both types of molecular markers were unequivocal in distinguishing two genetically distinct groups of individuals corresponding to their spatial separation. However, SSRs detected a higher level of subpopulation differentiation (F(ST) = 0.35, R(ST) = 0.32) than RAPDs (F(ST) = 0.21). SSR data indicated significant deviation from random dispersal of genes and genotypes between the two groups, suggesting that mating occurs mainly among individuals within subpopulations, thus, favouring the divergence between the two groups. This microevolutionary differentiation scenario might have been caused by a coupled effect of past genetic drift and reproductive isolation, as a result of strong glacial age bottlenecks and inefficient dispersal system of pollen and seeds, respectively. The identification of such genetic structure in this narrow endemic prompts a modification of the management strategies of its single extant population.

Conservation of Natural Resources↗

PubMed2006

Supertree analyses of the roles of viviparity and habitat in the evolution of atherinomorph fishes.

Using supertree phylogenetic reconstructions, we investigate how livebearing and freshwater adaptations may have shaped evolutionary patterns in the Atherinomorpha, a large clade (approximately 1500 extant species) of ray-finned fishes. Based on maximum parsimony reconstructions, livebearing appears to have evolved at least four times independently in this group, and no reversions to the ancestral state of oviparity were evident. With respect to habitat, at least five evolutionary transitions apparently occurred from freshwater to marine environments, at least two transitions in the opposite direction, and no clear ancestral state was identifiable. All viviparous clades exhibited more extant species than their oviparous sister taxa, suggesting that transitions to viviparity may be associated with cladogenetic diversification. Transitions to freshwater were usually, but not invariably associated with increased species richness, but the trend was, overall, not significant among sister clades. Additionally, we investigated whether livebearing and freshwater adaptations are currently associated with elevated risks of extinction as implied by species' presence on the 2004 IUCN Red List. Despite being correlated with decreased brood size, livebearing has not significantly increased extinction risk in the Atherinomorpha. However, freshwater species were significantly more likely than marine species to be listed as endangered.

Animals↗

PubMed2006

Assessing the effectiveness of reserve acquisition programs in protecting rare and threatened species.

Measuring the effectiveness of reserve networks is essential to ensure that conservation objectives such as species persistence are being met. We devised a new approach for measuring the effectiveness of land conservation in protecting rare and threatened species and applied it to an ecosystem of global significance. We compiled detailed global distributional data for 36 rare and threatened plants and animals found in the Lake Wales Ridge ecosystem in central Florida (U.S.A.). For each species, we developed a set of protection indices based in part on criteria used to categorize species for the World Conservation Union's Red List. We calculated protection indexes under three different conservation scenarios: a past scenario, which assumed recent, major land-acquisition efforts never occurred; a current scenario, which assumed no additional areas are saved beyond what is currently protected; and a targeted scenario, which assumed all of the remaining areas targeted for protection are eventually acquired. This approach enabled us to quantify the progress, in terms of reduced risk of extinction, that conservationists have made in protecting target species. It also revealed the limited success these land-acquisition efforts have had in reducing those extinction risks associated with loss of habitat or small geographic ranges. Many species of the Lake Wales Ridge will remain at high risk of extinction even if planned land-acquisition efforts are completely successful. By calculating protection indexes with and without each site for all imperiled species, we also quantified the contribution of each protected area to the conservation of each species, enabling local conservation decisions to be made in the context of a larger (global) perspective. The protection index approach can be adapted readily to other ecosystems with multiple rare and threatened species.

Animals↗

PubMed2025

Persistent Genomic Erosion in Whooping Cranes Despite Demographic Recovery.

Integrating in-situ (wild) and ex-situ (captive) conservation efforts can mitigate genetic diversity loss and help prevent extinction of endangered wild populations. The whooping crane (Grus americana) experienced severe population declines in the 18th century, culminating in a collapse to ~20 individuals by 1944. Legal protections and conservation actions have since increased the census population from a stock of 16 individuals to approximately 840 individuals, yet the impact on genomic diversity remains unclear. We analysed the temporal dynamics of genomic erosion by sequencing a high-quality reference genome, and re-sequencing 16 historical (years 1867-1893) and 37 modern (2007-2020) genomes, including wild individuals and four generations of captive-bred individuals. Genomic demographic reconstructions reveal a steady decline, accelerating over the past 300 years with the European settlement of North America. Temporal genomic analyses show that despite demographic recovery, the species has lost 70% of its historical genetic diversity and has increased its inbreeding. Although the modern population bottleneck reduced the ancestral genetic load, modern populations possess more realised load than masked load, possibly resulting in a chronic loss of fitness. Integrating pedigree and genomic data, we underscore the role of breeding management in reducing recent inbreeding. Yet ongoing heterozygosity loss, load accumulation, and persistent effects of historical inbreeding (i.e., background inbreeding) argue against the species' downlisting from its current Endangered status on the IUCN Red List and the Endangered Species Act. The presence of private genetic variation in wild and captive populations suggests that wild-captive crosses could enhance genetic diversity and reduce the realised load. Our findings emphasise the role of genomics in informing conservation management and policy.

Animals↗

PubMed2006

Modeling biodiversity dynamics in countryside landscapes.

The future of biodiversity hinges to a great extent on the conservation value of countryside, the growing fraction of Earth's surface heavily influenced by human activities. How many species, and which species, can persist in such landscapes (and analogous seascapes) are open questions. Here we explore two complementary theoretical frameworks to address these questions: species-area relationships and demographic models. We use the terrestrial mammal fauna of Central America to illustrate the application of both frameworks. We begin by proposing a multi-habitat species-area relationship, the countryside species-area relationship, to forecast species extinction rates. To apply it, we classify the mammal fauna by affinity to native and human-dominated habitats. We show how considering the conservation value of countryside habitats changes estimates derived from the classic species-area approach We also examine how the z value of the species-area relationship affects extinction estimates. Next, we present a framework for assessing the relative vulnerability of species to extinction in the countryside, based on the Skellam model of population dynamics. This model predicts the minimum area of contiguous native habitat required for persistence of a species, which we use as an indicator of vulnerability to habitat change. To apply the model, we use our habitat affinity classification of mammals and we estimate life-history parameters by species and habitat type. The resulting ranking of vulnerabilities is significantly correlated with the World Conservation Union (IUCN) Red List assessment.

Animals↗