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opencc-zeroDec 2016View details →

Data from: Evidence of opposing fitness effects of parental heterozygosity and relatedness in a critically endangered marine turtle?

How individual genetic variability relates to fitness is important in understanding evolution and the processes affecting populations of conservation concern. Heterozygosity-fitness correlations (HFCs) have been widely used to study this link in wild populations, where key parameters that affect both variability and fitness, such as inbreeding, can be difficult to measure. We used estimates of parental heterozygosity and genetic similarity ('relatedness') derived from 32 microsatellite markers to explore the relationship between genetic variability and fitness in a population of the critically endangered hawksbill turtle, Eretmochelys imbricata. We found no effect of maternal MLH (multilocus heterozygosity) on clutch size or egg success rate, and no single-locus effects. However, we found effects of paternal MLH and parental relatedness on egg success rate that interacted in a way that may result in both positive and negative effects of genetic variability. Multicollinearity in these tests was within safe limits, and null simulations suggested the effect was not an artefact of using paternal genotypes reconstructed from large samples of offspring. Our results could imply a tension between inbreeding and outbreeding depression in this system, which is biologically feasible in turtles: female-biased natal philopatry may elevate inbreeding risk and local adaptation, and both processes may be disrupted by male-biased dispersal. Although this conclusion should be treated with caution due to a lack of significant identity disequilibrium, our study shows the importance of considering both positive and negative effects when assessing how variation in genetic variability affects fitness in wild systems.

opencc-zeroDec 2016View details →

Data from: AFLP diversity and spatial structure of Calycophyllum candidissimum (Rubiaceae), a dominant tree species of Nicaragua's critically endangered seasonally dry forest

The Central American seasonally dry tropical (SDT) forest biome is one of the worlds' most endangered ecosystems, yet little is known about the genetic consequences of its recent fragmentation. A prominent constituent of this biome is Calycophyllum candidissimum, an insect-pollinated and wind-dispersed canopy tree of high socio-economic importance, particularly in Nicaragua. Here, we surveyed amplified fragment length polymorphisms across 13 populations of this species in Nicaragua to elucidate the relative roles of contemporary vs historical factors in shaping its genetic variation. Genetic diversity was low in all investigated populations (mean HE=0.125), and negatively correlated with latitude. Overall population differentiation was moderate (ΦST=0.109, P<0.001), and Bayesian analysis of population structure revealed two major latitudinal clusters (I: 'Pacific North'+'Central Highland'; II: 'Pacific South'), along with a genetic cline between I and II. Population-based cluster analyses indicated a strong pattern of 'isolation by distance' as confirmed by Mantel's test. Our results suggest that (1) the low genetic diversity of these populations reflects biogeographic/population history (colonisation from South America, Pleistocene range contractions) rather than recent human impact; whereas (2) the underlying process of their isolation by distance pattern, which is best explained by 'isolation by dispersal limitation', implies contemporary gene flow between neighbouring populations as likely facilitated by the species' efficient seed dispersal capacity. Overall, these results underscore that even tree species from highly decimated forest regions may be genetically resilient to habitat fragmentation due to species-typical dispersal characteristics, the necessity of broad-scale measures for their conservation notwithstanding.

opencc-zeroDec 2015View details →

Data from: No signs of inbreeding despite long-term isolation and habitat fragmentation in the critically endangered Montseny brook newt (Calotriton arnoldi)

Endemic species with restricted geographic ranges potentially suffer the highest risk of extinction. If these species are further fragmented into genetically isolated subpopulations, the risk of extinction is elevated. Habitat fragmentation is generally considered to have negative effects on species survival, despite some evidence for neutral or even positive effects. Typically, non-negative effects are ignored by conservation biology. The Montseny brook newt (Calotriton arnoldi) has one of the smallest distribution ranges of any European amphibian (8 km2) and is considered critically endangered by the International Union for Conservation of Nature. Here we apply molecular markers to analyze its population structure and find that habitat fragmentation owing to a natural barrier has resulted in strong genetic division of populations into two sectors, with no detectable migration between sites. Although effective population size estimates suggest low values for all populations, we found low levels of inbreeding and relatedness between individuals within populations. Moreover, C. arnoldi displays similar levels of genetic diversity to its sister species Calotriton asper, from which it separated around 1.5 million years ago and which has a much larger distribution range. Our extensive study shows that natural habitat fragmentation does not result in negative genetic effects, such as the loss of genetic diversity and inbreeding on an evolutionary timescale. We hypothesize that species in such conditions may evolve strategies (for example, special mating preferences) to mitigate the effects of small population sizes. However, it should be stressed that the influence of natural habitat fragmentation on an evolutionary timescale should not be conflated with anthropogenic habitat loss or degradation when considering conservation strategies.

opencc-zeroDec 2014View details →

Data from: Genetic variation, multiple paternity and measures of reproductive success in the critically endangered hawksbill turtle (Eretmochelys imbricata)

The Yucatán Peninsula in Mexico contains some of the largest breeding groups of the globally distributed and critically endangered hawksbill turtle (Eretmochelys imbricata). An improved understanding of the breeding system of this species and how its genetic variation is structured among nesting areas is required before the threats to its survival can be properly evaluated. Here, we genotype 1195 hatchlings and 41 nesting females at 12 microsatellite loci to assess levels of multiple paternity, genetic variation and whether individual levels of homozygosity are associated with reproductive success. Of the 50 clutches analyzed, only 6% have multiple paternity. The distribution of pairwise relatedness among nesting localities (rookeries) was not random with elevated within-rookery relatedness, and declining relatedness with geographic distance indicating some natal philopatry. Although there was no strong evidence that particular rookeries had lost allelic variation via drift, younger turtles had significantly lower levels of genetic variation than older turtles, suggesting some loss of genetic variation. At present there is no indication that levels of genetic variation are associated with measures of reproductive success such as clutch size, hatching success, and frequency of infertile eggs.

opencc-zeroDec 2013View details →

Data from: Critically endangered island endemic or peripheral population of a widespread species? Conservation genetics of Kikuchi's gecko and the global challenge of protecting peripheral oceanic island endemic vertebrates

Aim: To highlight the significant conservation challenge of evaluating peripheral endemic vertebrates in island archipelago systems and to assess empirically the complexities of approaches to conservation genetic studies across political and biogeographic boundaries. To demonstrate the poignant need for international collaboration and coordination when species delimitation problems with high conservation concern involve island endemics with biogeographically peripheral ranges. Location: Southeast Asia, Lanyu Island, Taiwan, and the Philippines. Methods: Genetic samples were collected and sequenced for one mitochondrial gene and five nuclear loci for species of the Gekko mindorensis-G. kikuchii species complex in Southeast Asia. We used maximum likelihood and Bayesian phylogenetic methods and coalescent-based species delimitation analyses to estimate phylogeographic relationships, construct multilocus haplotype networks and test putative species boundaries. Results: Phylogenetic and population genetic analyses suggest that Kikuchi's Gecko may represent a peripheral population of a widespread species distributed from the northern Philippines to Taiwan. However, we identify a discrepancy between inferences of species boundaries resulting from methods based on allele frequencies versus coalescent-based methods that incorporate evolutionary history. Coalescent-based analyses suggest that G. kikuchii may be a distinct evolutionary lineage. Our study underscores the need for coalescent-based methods in conjunction with population genetic approaches for conservation genetic assessments of widespread species. Main conclusions: This study joins a few recent works suggesting that Philippine-derived anomalies in the fauna of Lanyu (and possibly greater Taiwan) are worthy of careful reconsideration. Determining whether each is the result of recent human-mediated introduction or (possibly more ancient) natural dispersal should be the goal of future studies on this seldom-conceived biogeographic relationship. Isolated species endemic to islands on the outer periphery of biogeographic and political regions represent particular conservation challenges. This is especially true if a species occurs on an isolated island that is allied biogeographically with one nation, but politically administered by another.

opencc-zeroDec 2013View details →

Data from: Genetic evidence of hybridization between the critically endangered Cuban crocodile and the American crocodile: implications for population history and in situ/ex situ conservation

Inter-specific hybridization may be especially detrimental when one species is extremely rare and the other is abundant owing to the potential for genetic swamping. The Cuban crocodile (Crocodylus rhombifer) is a critically endangered island endemic largely restricted to Zapata Swamp, where it is sympatric with the widespread American crocodile (C. acutus). An on-island, C. rhombifer captive breeding program is underway with the goals of maintaining taxonomic integrity and providing a source of individuals for reintroduction, but its conservation value is limited by lack of genetic information. Here we collected mtDNA haplotypic and nuclear genotypic data from wild and captive C. rhombifer and C. acutus in Cuba to: (1) investigate the degree of inter-specific hybridization in natural (in situ) and captive (ex situ) populations; (2) quantify the extent, distribution and in situ representation of genetic variation ex situ; and (3) reconstruct founder relatedness to inform management. We found high levels of hybridization in the wild (49.1%) and captivity (16.1%), and additional evidence for a cryptic lineage of C. acutus in the Antilles. We detected marginally higher observed heterozygosity and allelic diversity ex situ relative to the wild population, with captive C. rhombifer exhibiting over twice the frequency of private alleles. Although mean relatedness was high in captivity, we identified 37 genetically important individuals that possessed individual mean kinship (MK) values lower than the population MK. Overall, these results will guide long-term conservation management of Cuban crocodiles for maintaining the genetic integrity and viability of this species of high global conservation value.

opencc-zeroDec 2011View details →

Data from: Circumpolar diversity and geographic differentiation of mtDNA in the critically endangered Antarctic blue whale (Balaenoptera musculus intermedia)

The Antarctic blue whale (Balaenoptera musculus intermedia) was hunted to near extinction between 1904 and 1972, declining from an estimated initial abundance of more than 250,000 to fewer than 400. Here, we describe mtDNA control region diversity and geographic differentiation in the surviving population of the Antarctic blue whale, using 218 biopsy samples collected under the auspices of the International Whaling Commission (IWC) during research cruises from 1990–2009. Microsatellite genotypes and mtDNA sequences identified 166 individuals among the 218 samples and documented movement of a small number of individuals, including a female that traveled at least 6,650 km or 131° longitude over four years. mtDNA sequences from the 166 individuals were aligned with published sequences from 17 additional individuals, resolving 52 unique haplotypes from a consensus length of 410 bp. From this minimum census, a rarefaction analysis predicted that only 72 haplotypes (95% CL, 64, 86) have survived in the contemporary population of Antarctic blue whales. However, haplotype diversity was relatively high (0.968±0.004), perhaps as a result of the longevity of blue whales and the relatively recent timing of the bottleneck. Despite the potential for circumpolar dispersal, we found significant differentiation in mtDNA diversity (FST = 0.032, p<0.005) and microsatellite alleles (FST = 0.005, p<0.05) among the six Antarctic Areas historically used by the IWC for management of blue whales.

FIGURE 9 in A new handfish, Brachionichthys australis sp. nov. (Lophiiformes: Brachionichthyidae), with a redescription of the critically endangered spotted handfish, B. hirsutus (Lacepède)

FIGURE 9. Unusual, persistent juvenile colour morph of Brachionichthys hirsutus, ca. 39 mm TL. Image courtesy of Mark Green (CSIRO).

FIGURE 3. K2P in A new handfish, Brachionichthys australis sp. nov. (Lophiiformes: Brachionichthyidae), with a redescription of the critically endangered spotted handfish, B. hirsutus (Lacepède)

FIGURE 3. K2P distance neighbour-joining tree of cytochrome oxidase I sequences from Brachionichthys australis sp. nov., B. hirsutus, Lophiodes cf mutilus and Sladenia sp. Bootstrap values less than 80% not shown.

FIGURE 6 in A new handfish, Brachionichthys australis sp. nov. (Lophiiformes: Brachionichthyidae), with a redescription of the critically endangered spotted handfish, B. hirsutus (Lacepède)

FIGURE 6. Female Brachionichthys hirsutus attending egg mass. Egg mass attached to an artificial holdfast. Image courtesy of Mark Green (CSIRO).

FIGURE 8 in A new handfish, Brachionichthys australis sp. nov. (Lophiiformes: Brachionichthyidae), with a redescription of the critically endangered spotted handfish, B. hirsutus (Lacepède)

FIGURE 8. Newly hatched Brachionichthys hirsutus, ca. 30 mm TL, specimens from captive breeding program. Image courtesy of Mark Green (CSIRO).

FIGURE 7 in A new handfish, Brachionichthys australis sp. nov. (Lophiiformes: Brachionichthyidae), with a redescription of the critically endangered spotted handfish, B. hirsutus (Lacepède)

FIGURE 7. Developing Brachionichthys hirsutus in egg capsules prior to hatching. Egg mass attached to an artificial holdfast. Image courtesy of Mark Green (CSIRO).

FIGURE 5 in A new handfish, Brachionichthys australis sp. nov. (Lophiiformes: Brachionichthyidae), with a redescription of the critically endangered spotted handfish, B. hirsutus (Lacepède)

FIGURE 5. Skin from left side of a preserved specimen of Brachionichthys hirsutus, CSIRO H 6564-01, 63.9 mm SL.

FIGURE 4 in A new handfish, Brachionichthys australis sp. nov. (Lophiiformes: Brachionichthyidae), with a redescription of the critically endangered spotted handfish, B. hirsutus (Lacepède)

FIGURE 4. Brachionichthys hirsutus, lateral view: A. MNHN A 4627, lectotype, 78.7 mm SL; and B. composite illustration © R. Swainston, www.anima.net.au.

FIGURE 2 in A new handfish, Brachionichthys australis sp. nov. (Lophiiformes: Brachionichthyidae), with a redescription of the critically endangered spotted handfish, B. hirsutus (Lacepède)

FIGURE 2. Scales from the left side of a cleared and stained specimen of Brachionichthys australis sp. nov., CSIRO H 4259-03, 44.7 mm SL.

FIGURE 1 in A new handfish, Brachionichthys australis sp. nov. (Lophiiformes: Brachionichthyidae), with a redescription of the critically endangered spotted handfish, B. hirsutus (Lacepède)

FIGURE 1. Brachionichthys australis sp. nov., lateral view: A. CSIRO H 4451-02, holotype, 45.9 mm SL; and B. composite illustration © R. Swainston, www.anima.net.au.

FIGURE 3 in A new subspecies of Batagur affinis (Cantor, 1847), one of the world's most critically endangered chelonians (Testudines: Geoemydidae)

FIGURE 3. (a) Batagur baska, male, Sundarbans, Bangladesh – photo: S.M.A. Rashid; (b) B. baska, semiadult female (the pointed, upturned snout develops only with increasing age), Sundarbans, Bangladesh – photo: P. Praschag; (c) west coast form of B. affinis, male, Klong La-ngu River, Satun Province, Thailand – photo: B. Horne; (d) west coast form of B. affinis, female, Perak River, Malaysia – photo: E.O. Moll; (e) east coast form of B. affinis, male, Dungun River, Malaysia – photo: E.H. Chan; (f) east coast form of B. affinis, female, Terengganu River, Malaysia – photo: E.O. Moll; (g) Cambodian Batagur male, Sre Ambel River system, Cambodia – photo: R. Holloway; (h) Cambodian Batagur female, Sre Ambel River system, Cambodia – photo: B. Horne. Note differences in head shape, soft part and iris coloration.

FIGURE 4 in A new subspecies of Batagur affinis (Cantor, 1847), one of the world's most critically endangered chelonians (Testudines: Geoemydidae)

FIGURE 4. Hatchlings of Batagur affinis, (a) west coast form, Perak River, Malaysia; (b) east coast form, Terengganu River, Malaysia – photos: E.O. Moll. Note yellow marginal scutes and silvery blotches in temporal and parietal region in the east coast hatchling.

FIGURE 2 in A new subspecies of Batagur affinis (Cantor, 1847), one of the world's most critically endangered chelonians (Testudines: Geoemydidae)

FIGURE 2. Parsimony networks for mitochondrial haplotypes of Batagur affinis, B. baska, B. kachuga, and the Cambodian Batagur (connection enforced). Symbol size corresponds to haplotype frequency; missing node haplotypes black. Lines joining haplotypes, one mutational step except otherwise indicated. (a) Network based on a 320-bp-long alignment of cyt b. Haplotypes and their frequencies (see Appendix): B. affinis – A1 (n=9), A2 (n=1); B. baska – B1 (n=5), B2 (n=1), B3 (n=1); B. kachuga – K1 (n=3), K2 (n=1), K3 (n=1); Cambodian Batagur – C (n=7). Haplotypes A1 and B1 include the lectotype of Tetraonyx affinis Cantor, 1847 and topotypic specimens of Emys baska Gray, 1830, respectively (Praschag et al. 2008). Haplotypes K1 and K2 are from topotypic specimens of Emys kachuga Gray, 1831. (b) Network based on a 1067-bp-long alignment of cyt b. Haplotypes and their frequencies: B. affinis – A1 (n=8), A2 (n=1); B. baska – B1 (n=4); B. kachuga – K1 (n=3), K2 (n=1), K3 (n=1); Cambodian Batagur – C (n=7).

FIGURE 5 in A new subspecies of Batagur affinis (Cantor, 1847), one of the world's most critically endangered chelonians (Testudines: Geoemydidae)

FIGURE 5. Historical distribution of Batagur affinis affinis, B. a. edwardmolli, and B. baska (modified from Praschag et al. 2008). Note that the species are extirpated in most of their former ranges.