Genetic analysis reveals population structure and recent migration within the highly fragmented range of the Cross River gorilla (Gorilla gorilla diehli)

Recently developed methods of individual-based analysis of genetic data allow an unprecedented opportunity to understand the relationships among fragmented populations. By defining population structure and identifying migrant individuals, such analyses can provide a framework to aid in evaluating the threats posed by inbreeding and reduced genetic variability as a consequence of limited gene flow among fragments. Here we investigate population structure in the critically endangered Cross River gorilla (Gorilla gorilla diehli) by applying a suite of individual-based analyses to data obtained from between one-quarter and one-third of the estimated total population through the use of noninvasively collected DNA samples. The population structure inferred using data from 11 autosomal microsatellite loci was broadly consistent with geography and habitat fragmentation, but showed no simple isolation-by-distance effects. In contrast to previous field surveys, which suggested that all gorilla localities were isolated from one another, we infer low levels of gene flow and identify migrants between habitat fragments as well as individuals of admixed ancestry, suggesting persistent recent reproductive contact between many of the localities. These results are encouraging for the conservation of the Cross River gorilla population. Conservation efforts should strive to maintain connectivity between subpopulations that are still in migratory contact and attempt to restore connectivity where it has been lost.     

Contemporary breeding biology of critically endangered Regent Honeyeaters: implications for conservation

Identifying factors influencing the demographics of threatened species is essential for conservation, but a lack of comprehensive demographic data often impedes the effective conservation of rare and mobile species. We monitored breeding of critically endangered and semi‐nomadic Regent Honeyeaters Anthochaera phrygia (global population c. 100 pairs) over 3 years throughout their range. Overall nest success probability (0.317) was highly spatially variable and considerably lower than previous estimates for this (and many other honeyeater) species, as was productivity of successful nests (mean 1.58 juveniles fledged). Nest surveillance revealed high predation rates by a range of birds and arboreal mammals as the primary cause of nest failure. An estimated 12% of pairs either failed to establish a territory or their nests did not reach the egg stage. We also found a male bias to the adult sex ratio, with an estimated 1.18 males per female. Juvenile survival for the first 2 weeks after fledging was high (86%). Management interventions that aim to increase nest success in areas of low nest survival must be investigated to address an apparent decline in reproductive output and avoid extinction of the Regent Honeyeater. We show that temporal and spatial variation in the breeding success of rare and highly mobile species can be quantified with robust population monitoring using sampling regimens that account for their life histories. Understanding the causes of spatio‐temporal variation in breeding success can enhance conservation outcomes for such species through spatially and temporally targeted recovery actions.     

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.     

Tourism as a threat to critically endangered and endangered birds: global patterns and trends in conservation hotspots

More than 12 % of bird species are threatened with extinction. Numerous anthropogenic activities and processes are considered responsible for such declines, including tourism related activities. These activities often occur in global biodiversity hotspots but few studies consider the potential risks associated with tourism. The relative importance of tourism as a threat to birds was quantified using a global analysis of the threats facing critically endangered and endangered birds in the hotspots. Sixty-three critically endangered and endangered bird species are reportedly threatened by tourism. Among those 63 species, marine, coastal and aquatic birds are threatened more by tourism than was expected. Hotspots with the most species threatened by tourism are Polynesia–Micronesia and the Mediterranean Basin. This study uses individual threatening processes in a new way to characterise hotspots for conservation action, advancing previous identification criteria. Analysing hotspots in terms of the relative presence of individual threatening processes may help to more effectively direct future research in these priority regions.     

Population and geographic range dynamics: implications for conservation planning

Continuing downward trends in the population sizes of many species, in the conservation status of threatened species, and in the quality, extent and connectedness of habitats are of increasing concern. Identifying the attributes of declining populations will help predict how biodiversity will be impacted and guide conservation actions. However, the drivers of biodiversity declines have changed over time and average trends in abundance or distributional change hide significant variation among species. While some populations are declining rapidly, the majority remain relatively stable and others are increasing. Here we dissect out some of the changing drivers of population and geographic range change, and identify biological and geographical correlates of winners and losers in two large datasets covering local population sizes of vertebrates since 1970 and the distributions of Galliform birds over the last two centuries. We find weak evidence for ecological and biological traits being predictors of local decline in range or abundance, but stronger evidence for the role of local anthropogenic threats and environmental change. An improved understanding of the dynamics of threat processes and how they may affect different species will help to guide better conservation planning in a continuously changing world.     

Translocation as an ultimate conservation measure for the long-term survival of a critically endangered freshwater mussel

Hydrobiologia - Pseudunio auricularius (Spengler, 1793) is one of the most threatened unionid species worldwide. Translocation is considered one of the ultimate actions that can save this species...     

Using predictive modelling to guide the conservation of a critically endangered coastal wetland amphibian

Amphibians are the most threatened Class of vertebrate, with wetland-associated anurans in particular suffering high levels of habitat loss. We used predictive modelling to better understand the distribution of a critically endangered South African endemic (Hyperolius pickersgilli) and to guide conservation action. MaxEnt distribution models were produced based on limited occurrence data. Predicted localities with probability of occurrence ≥60% were surveyed. Ten new sub-populations were discovered. The mean probability of occurrence for the species at wetlands where it was detected was greater than that at wetlands where it was not detected or absent. In addition, 17 known historical localities were re-visited and the species deemed absent at 8 of these. The total number of localities at which the species is now known to occur is 18, which is an increase in the known extant sub-populations of six. We recalculate the area of occupancy and extent of occurrence for the species as 108 km² and 2081.5 km², respectively; both increases on previous estimates. Implications of these changes on the IUCN Red List status of H. pickersgilli are discussed. A friction map was created to identify possible linkages between sub-populations, which can be used to guide habitat restoration and population repatriation. Given the degree of isolation of subpopulations and the potentially severe threats to most of these, urgent conservation action for H. pickersgilli remains crucial. This study provides a method for use in conservation planning for wetland-breeding amphibians in eastern coastal regions of Africa and elsewhere.     

When rediscovery is not enough: taxonomic uncertainty hinders conservation of a critically endangered bird

In 2003, birds similar to the extinct New Zealand storm-petrel Oceanites maorianus were observed in Hauraki Gulf NZ, raising the possibility of rediscovery after 150 years. O. maorianus has and continues to be surrounded by taxonomic uncertainty, being variously described as a distinct genus, a distinct species, or merely a plumage variant. This uncertainty has hindered conservation planning and funding for the species. Here we examine the taxonomic identity of the rediscovered birds and museum specimens using phylogenetic analysis of mitochondrial (1143 bp cytochrome b) and nuclear (890 bp β-fibrinogen) genes. Using cytochrome b sequence amplified from the 150+ year old specimens, we found that the extant and museum O. maorianus were the same taxon (0.01 genetic distance), with both differing from all other storm-petrel taxa. Using both genes, we examined the phylogenetic affinities of O. maorianus to the Oceanitinae and Hydrobatinae storm-petrels finding that O. maorianus was more closely aligned to Fregetta (0.08-0.09) than Oceanites (0.11-0.12), thereby confirming its status as a distinct taxon, not a plumage variant of O. oceanicus. Our analysis verifies that the previously presumed extinct New Zealand storm-petrel has been rediscovered and can now be assigned a conservation priority commensurate with its critically endangered status.     

Managing polyploidy in ex situ conservation genetics: the case of the critically endangered Adriatic sturgeon (Acipenser naccarii)

While the current expansion of conservation genetics enables to address more efficiently the management of threatened species, alternative methods for genetic relatedness data analysis in polyploid species are necessary. Within this framework, we present a standardized and simple protocol specifically designed for polyploid species that can facilitate management of genetic diversity, as exemplified by the ex situ conservation program for the tetraploid Adriatic sturgeon Acipenser naccarii. A critically endangered endemic species of the Adriatic Sea tributaries, its persistence is strictly linked to the ex situ conservation of a single captive broodstock currently decimated to about 25 individuals, which represents the last remaining population of Adriatic sturgeon of certain wild origin. The genetic variability of three F1 broodstocks available as future breeders was estimated based on mitochondrial and microsatellite information and compared with the variability of the parental generation. Genetic data showed that the F1 stocks have only retained part of the genetic variation present in the original stock due to the few parent pairs used as founders. This prompts for the urgent improvement of the current F1 stocks by incorporating new founders that better represent the genetic diversity available. Following parental allocation based on band sharing values, we set up a user-friendly tool for selection of candidate breeders according to relatedness between all possible parent-pairs that secures the use of non-related individuals. The approach developed here could also be applied to other endangered tetraploid sturgeon species overexploited for caviar production, particularly in regions lacking proper infrastructure and/or expertise.     

Genetic fingerprinting of germplasm accessions as an aid for species conservation: a case study with Borderea chouardii (Dioscoreaceae), one of the most critically endangered Iberian plants

BACKGROUND AND AIMS: Molecular markers have changed previous expectations about germplasm collections of endangered plants, as new perspectives aim at holding a significant representation of all the genetic diversity in the studied species to accomplish further conservation initiatives successfully. Borderea chouardii is a critically endangered allotetraploid dioecious member of Dioscoreaceae, known from a single population in the Iberian pre-Pyrenees. This population was reported to be highly structured into two genetically distinct groups of individuals corresponding to their spatial separation along the vertical cliff where it grows. In 1999, the Spanish Government of Aragón launched the first conservation programme for the ex situ preservation of this species, and since then a seed collection has been conserved at the Germplasm Bank of the Universidad Politécnica de Madrid. However, as some seed samples had not been labelled clearly at the time of collection, their origin was uncertain. METHODS: Genetic variation in germplasm accessions of B. chouardii was investigated using microsatellite (simple sequence repeat; SSR) markers. KEY RESULTS: The 17 primer pairs used detected 62 SSR alleles in the 46 samples analysed from five different germplasm stocks. Eight alleles scored from the wild population were not detected in the germplasm samples analysed. The relatedness of the germplasm samples to the wild subpopulations through neighbour-joining clustering, principal coordinates analysis (PCO) and assignment tests revealed a biased higher representation of the genetic diversity of the lower cliff (43 samples) subpopulation than that of the upper cliff (three samples). CONCLUSIONS: The collection of additional samples from the upper cliff is recommended to achieve a better representation of the genetic diversity of this subpopulation. It is also recommended that these stocks should be managed separately according to their distinct microspatial origin in order to preserve the genetic substructuring of the wild population.     

Autogamous seed set in a critically endangered orchid in Japan: pollination studies for the conservation of Nervilia nipponica

The pollination biology of the critically endangered Nervilia nipponica was investigated at two sites on Shikoku Island, Japan, to shed light on the species' ecological strategy and to help prioritise management decisions for its conservation. Though the solitary flowers failed to attract pollinators, high rates of fruit set were observed in control plants at both sites. Comparable rates were obtained in bagged plants and following induced autogamous and xenogamous pollinations, indicating that the species is capable of outbreeding, but self-compatible and not pollinator-limited for fruit set under natural conditions; rates were significantly lower following emasculation. The number of seeds set per fruit and their fertility did not differ significantly between open-, self- and cross-pollinated treatments. Epifluorescence microscopy revealed that, in open-pollinated plants, pollen grains germinate within the anther on the first day of anthesis, and that fertilisation occurs within the following 96 hours. The position of the stigma, which overlaps the clinandrium, friable pollinia, and the absence of a rostellum ensure efficient, non-mechanical autopollination. Though this confers reproductive assurance, inbreeding depression may be limiting fitness at subsequent stages of the recruitment cycle and low genetic diversity is inferred.     

High genetic structure of the Cozumel Harvest mice,a critically endangered island endemic: conservation implications

We assessed the genetic structure and diversity of Reithrodontomys spectabilis, a critically endangered, endemic rodent from Cozumel Island, México. A total of 90 individuals were trapped from September 2001 to January 2005. Microsatellite data analysis revealed high genetic diversity values: a total of 113 alleles (average 12.5 per locus), H _o  = 0.78, H _e  = 0.80. These high values can be related to Cozumel’s size (478 km²) and extensive native vegetation cover, factors that could be promoting a suitable population size, high heterozygosity and the persistence of rare alleles in the species, as well as some long-term movement of individuals between sampling localities. A strong genetic structure was also observed, with at least four genetic groups, associated with a pattern of isolation by distance. We found a strong allelic and genetic differentiation shown between localities, with negligible recent gene flow and low inbreeding coefficients. The species life history and ecological characteristics—being nocturnal, semi-terrestrial, a good tree climber, having lunar phobia and significant edge effect—are likely affecting its genetic structure and differentiation. The high genetic diversity and population structure award R. spectabilis a significant conservation value. Our results can serve as a basis for future research and conservation of the species, particularly considering the problems the island is facing from habitat perturbation, urbanization and introduction of exotic species. In view of the structure and genetic variability observed, it is essential to establish and reinforce protected areas and management programs for the conservation of the endemic and endangered Cozumel Harvest mice.     

Climate-driven range expansion of a critically endangered top predator in northeast Atlantic waters

Global climate change is driving rapid distribution shifts in marine ecosystems; these are well established for lower trophic levels, but are harder to quantify for migratory top predators. By analysing a 25-year sightings-based dataset, we found evidence for rapid northwards range expansion of the critically endangered Balearic shearwater Puffinus mauretanicus in northeast Atlantic waters. A 0.6 degrees C sea surface temperature increase in the mid-1990s is interpreted as an underlying controlling factor, while simultaneous northward shifts of plankton and prey fish species suggests a strong bottom-up control. Our results have important conservation implications and provide new evidence for climate-driven regime shift in Atlantic ecosystems.     

Genetic diversity in fragmented populations of the critically endangered spider orchid Caladenia huegelii: implications for conservation

The Orchidaceae is characterised by a diverse range of life histories, reproductive strategies and geographic distribution, reflected in a variety of patterns in the population genetic structure of different species. In this study, the genetic diversity and structure was assessed within and among remnant populations of the critically endangered sexually deceptive orchid, Caladenia huegelii. This species has experienced severe recent habitat loss in a landscape marked by ancient patterns of population fragmentation within the Southwest Australian Floristic Region, a global biodiversity hotspot. Using seven polymorphic microsatellite loci, high levels of within-population diversity (mean alleles/locus = 6.73; mean H _E = 0.690), weak genetic structuring among 13 remnant populations (F _ST = 0.047) and a consistent deficit of heterozygotes from Hardy–Weinberg expectation were found across all populations (mean F _IS = 0.22). Positive inbreeding coefficients are most likely due to Wahlund effects and/or inbreeding effects from highly correlated paternity and typically low fruit set. Indirect estimates of gene flow (Nm = 5.09 using F _ST; Nm = 3.12 using the private alleles method) among populations reflects a historical capacity for gene flow through long distance pollen dispersal by sexually deceived wasp pollinators and/or long range dispersal of dust-like orchid seed. However, current levels of gene flow may be impacted by habitat destruction, fragmentation and reduced population size. A genetically divergent population was identified, which should be a high priority for conservation managers. Very weak genetic differentiation indicates that the movement and mixing of seeds from different populations for reintroduction programs should result in minimal negative genetic effects.     

Genetic diversity and differentiation in the critically endangered orchid (Amitostigma hemipilioides): implications for conservation

Amitostigma hemipilioides is an endangered terrestrial orchid endemic to China. In the Southwestern China, the species is found restricted growing in the karst limestone or rock in the edge of farmland, moist hillsides or river. In the present study, the genetic diversity and differentiation was estimated within and among habitats, populations and groups of this species by ISSR markers. Using 13 polymorphic primers, an intermediate level of genetic diversity was found at the species level and population level with the percentage of polymorphic bands (P) of 64.7 and 50.9 %, Shannon index of diversity (I) of 0.3873 and 0.2949, respectively. The analysis of molecular variance (AMOVA) showed that the high level of population differentiation was presented with 45.63 % relative to the total genetic variation residing among eight populations. It was noteworthy that as much as 69.17 % of the total diversity was most likely attributed to the difference among the populations in fragmentation habitat conditions, while 16.32 % of the total diversity could be attributed to the difference among the populations in stable and favorable habitat conditions. The in situ conservation is a top strategy, thus the mycorrhizal fungi and pollinators are protected by protecting habitat and avoiding fragmentation which is helpful to the cycle of this endangered orchid species and recovery of its wild populations. In addition, to maintaining the germplasm bank of this species, the ex situ conservation by habitat simulation and reintroduction has been considered in the living collection at Kaili University ecological garden and Yuntai Mountain scenic spot using the plants collected in this study.     

Protecting persistent dynamic oceanographic features: transboundary conservation efforts are needed for the critically endangered Balearic shearwater

The protection of key areas for biodiversity at sea is not as widespread as on land and research investment is necessary to identify biodiversity hotspots in the open ocean. Spatially explicit conservation measures such as the creation of representative networks of marine protected areas (MPAs) is a critical step towards the conservation and management of marine ecosystems, as well as to improve public awareness. Conservation efforts in ecologically rich and threatened ecosystems are specially needed. This is particularly urgent for the Mediterranean marine biodiversity, which includes highly mobile marine vertebrates. Here, we studied the at sea distribution of one of the most endangered Mediterranean seabird, the critically endangered Balearic shearwater Puffinus mauretanicus. Present knowledge, from vessel-based surveys, suggests that this species has a coastal distribution over the productive Iberian shelf in relation to the distribution of their main prey, small pelagic fish. We used miniaturised satellite transmitters to determine the key marine areas of the southern population of Balearic shearwaters breeding on Eivissa and spot the spatial connections between breeding and key marine areas. Our tracking study indicates that Balearic shearwaters do not only forage along the Iberian continental shelf but also in more distant marine areas along the North African coast, in particular W of Algeria, but also NE coast of Morocco. Birds recurrently visit these shelf areas at the end of the breeding season. Species distribution modelling identified chlorophyll a as the most important environmental variable in defining those oceanographic features characterizing their key habitats in the western Mediterranean. We identified persistent oceanographic features across time series available in the study area and discuss our results within the current conservation scenario in relation to the ecology of the species.     

Maximizing species conservation in continental Ecuador: a case of systematic conservation planning for biodiverse regions

Ecuador has the largest number of species by area worldwide, but also a low representation of species within its protected areas. Here, we applied systematic conservation planning to identify potential areas for conservation in continental Ecuador, with the aim of increasing the representation of terrestrial species diversity in the protected area network. We selected 809 terrestrial species (amphibians, birds, mammals, and plants), for which distributions were estimated via species distribution models (SDMs), using Maxent. For each species we established conservation goals based on conservation priorities, and estimated new potential protected areas using Marxan conservation planning software. For each selected area, we determined their conservation priority and feasibility of establishment, two important aspects in the decision-making processes. We found that according to our conservation goals, the current protected area network contains large conservation gaps. Potential areas for conservation almost double the surface area of currently protected areas. Most of the newly proposed areas are located in the Coast, a region with large conservation gaps and irreversible changes in land use. The most feasible areas for conservation were found in the Amazon and Andes regions, which encompass more undisturbed habitats, and already harbor most of the current reserves. Our study allows defining a viable strategy for preserving Ecuador''s biodiversity, by combining SDMs, GIS-based decision-support software, and priority and feasibility assessments of the selected areas. This approach is useful for complementing protected area networks in countries with great biodiversity, insufficient biological information, and limited resources for conservation.