Protecting a single endangered species and meeting multiple conservation goals: an approach with Guaiacum sanctum in Yucatan Peninsula,Mexico

Aim New protected areas should consider safeguarding high conservation value sites based on multiple criteria and not just the presence of a single endangered or charismatic species. However, the extent to which complementary criteria coincide is usually unknown. We use the case of Guaiacum sanctum (Zygopyllaceae), an endangered timber tree species, to explore whether the protection of forests where this species is most abundant would meet other complementary conservation goals, such as capturing regional plant biodiversity, protecting other threatened/endemic species or safeguarding ecosystem services. Location Yucatan Peninsula, southern Mexico. Methods We conducted an analysis of the structure, composition and diversity of tree communities (including stems ≥5 cm dbh) at eight G. sanctum forest sites. We identified endemic and threatened tree species and quantified above‐ground tree biomass and carbon storage in these G. sanctum forests. Results Guaiacum sanctum forests contain 35–59 tree species on plots as small as 1000 m². The species composition of tree communities changed rapidly (high β‐diversity) across soil boundaries and rainfall regimes. Twenty‐one endemic and eight threatened tree species were recorded in our inventories. Individuals of G. sanctum represented up to 55% of the above‐ground carbon for trees ≥5 cm dbh. The high basal area of G. sanctum forests plus the high wood density, abundance, large size and longevity (more than 500 years) of G. sanctum and other tree species enhance the potential importance of these forests for carbon storage. Main conclusions A conservation strategy focused on protecting important populations of G. sanctum in the Yucatan Peninsula would have significant co‐benefits for conservation of regional tree species biodiversity and provision of critical ecosystem services. Our study illustrates a multiple criteria approach useful for the selection of areas with high conservation value on the basis of endemic, threatened species, species richness and ecosystem services.     

Exon-primed, intron-crossing (EPIC) loci for five nuclear genes in deep-sea protobranch bivalves: primer design, PCR protocols and locus utility

We describe PCR primers and amplification protocols developed to obtain introns from conserved nuclear genes in deep-sea protobranch bivalves. Because almost no sequence data for protobranchs are publically available, mollusk and other protostome sequences from GenBank were used to design degenerate primers, making these loci potentially useful in other invertebrate taxa. Amplification and sequencing success varied across the test group of 30 species, and we present five loci spanning this range of outcomes. Intron presence in the targeted regions also varied across genes and species, often within single genera; for instance, the calmodulin and β-tubulin loci contained introns with high frequency, whereas the triose phosphate isomerase locus never contained an intron. In introns for which we were able to obtain preliminary estimates of polymorphism levels in single species, polymorphism was greater than traditional mitochondrial loci. These markers will greatly increase the ability to assess population structure in the ecologically important protobranchs, and may prove useful in other taxa as well.     

Conservation Assessment of Guaiacum sanctum and Guaiacum coulteri: Historic Distribution and Future Trends in Mexico

Guaiacum sanctum and Guaiacum coulteri are long‐lived Mesoamerican timber tree species heavily exploited throughout their range and considered to be at risk of extinction. Both species are included on the IUCN Red List and on CITES Appendix II, but there has been no formal assessment of the conservation status of either species. We used ecological niche modeling and rapid assessments of local density and population size structure to provide such evaluations. For the year 2000, we estimated geographic range sizes for G. sanctum and G. coulteri of 95,422 and 130,973 km², respectively. The main core remaining habitat for G. sanctum occurs in Campeche State (Yucatan Peninsula), where populations exhibit high adult abundance and profuse regeneration. Several areas along the Mexican Pacific coast remain with suitable habitat for G. coulteri. Guaiacum coulteri is at greater risk as only 1.3 percent of its current habitat is protected, which contrasts with the 13.2 percent of current habitat protected for G. sanctum. We projected that available habitat for G. sanctum and G. coulteri will decline by a further 30–50 percent by 2020 if estimated habitat loss rates continue. We suggest that under the IUCN criteria, the conservation status of G. sanctum and G. coulteri should be updated to near threatened and vulnerable, respectively. Additionally, we conclude that the amount of protected habitat needs to be increased to safeguard both species. Our study provides a quantitative basis for updating the conservation status of both species and illustrates an assessment framework that could be applied to other threatened tree species.     

Eight polymorphic microsatellite markers for kelp bass,Paralabax clathratus,amplified in three multiplex polymerase chain reaction sets

Kelp bass, Paralabrax clathratus, is an important sport fishery of California, USA and Baja, Mexico. Here we describe eight microsatellite loci developed for this species. Two loci were derived from known primers for other species in the family, Serranidae and six were developed anew using a clone enrichment protocol. Loci were arranged into three multiplex PCR (polymerase chain reaction) sets for fast throughput; 564 individuals from nine populations across the species’ range were genotyped. Polymorphism ranged from four to 47 alleles and all populations at all loci displayed Hardy–Weinberg and linkage equilibrium.     

Polymorphic microsatellite loci in Eurytoma brunniventris,a generalist parasitoid in oak cynipid galls

Eurytoma brunniventris is a parasitic wasp with a wide range of host species. We have developed primers for nine polymorphic microsatellite loci to allow examination of intraspecific population subdivision associated with two aspects of the biology of their hosts: host species (oak gallwasps) and the tree on which the gallwasp develops (different oak species). All nine loci amplified well across individuals collected from a range of gallwasp species and across two oak taxa. These microsatellite loci are potentially of value in the study of closely related economic pests such as seed predators of almonds (E. amygdali) and pistachios (E. plotnikovi).     

Isolation, characterization and cross-amplification of polymorphic microsatellite loci in Laelia speciosa (Orchidaceae)

Laelia speciosa is an endangered epiphytic orchid endemic to central Mexico. Here, we report on the development of 14 perfect and imperfect microsatellite repeat loci for this species. Numbers of alleles ranged from two to 16 and levels of observed heterozygosities among the 14 loci ranged from 0.28 to 1.00 across two widely divergent populations. All loci were also tested for cross-amplification in four other Laelia species and other selected genera of the subtribe Laeliinae.     

Isolation and characterisation of 26 microsatellite loci from a widespread tropical hydrozoan,Macrorhynchia phoenicea (Leptothecata,Aglaopheniidae), and cross-amplification in closely related species

We isolated and characterized 26 microsatellite loci for Macrorhynchia phoenicea (Busk, 1852), a rather common tropical hydrozoan from the Indo-Pacific. The number of alleles per locus ranged from 4 to 24. The observed heterozygosity ranged from 0.000 to 0.970 and the expected heterozygosity from 0.029 to 0.833. Ten loci were at Hardy–Weinberg equilibrium. No pair of loci presented linkage disequilibrium. Transferability of up to 18 loci was positive across four other Aglaopheniidae species from different genera. These loci will be used in studying reef population connectivity for these particular species at the scale of the Indo-Pacific, a promising but little explored research field.     

Development of microsatellite markers in Dendrobium fimbriatum Hook, an endangered Chinese endemic herb

As an endangered endemic herb, Dendrobium fimbriatum, is under threat from numerous impacts. In order to analyse the genetic diversity and structure of this endangered species, we provide details of 10 microsatellite loci (out of 15 primer pairs designed) which showed polymorphic for D. fimbriatum. These loci were used to screen 25 individuals from across the species' geographical range. Ten loci were polymorphic with 2 to 19 alleles; three loci were monomorphic, while the rest produced no amplification fragments. These loci will be used to investigate population genetic structure, genetic diversity, conservation, and individual authentication in the endangered D. fimbriatum.     

Cross-amplification and characterization of microsatellite loci for the Neotropical orchid genus Epidendrum

In this study we tested the cross-amplification of 33 microsatellite loci previously developed for two closely related Neotropical orchid genera (Epidendrum and Laelia). A set of ten loci were polymorphic across five examined species (20 individuals each) with 2 to 15 alleles per locus. The mean expected and observed heterozygosity (average across species) ranged from 0.34 to 0.82 and from 0.27 to 0.85, respectively. In addition we tested all loci in 35 species representative of the genus Epidendrum. Of these, 26 loci showed successful amplification. Cross-application of these loci represent a potential source of co-dominant markers for evolutionary, ecological and conservation studies in this important orchid genus.     

Twenty-two polymorphic microsatellite loci aimed at detecting illegal trade in the Cape parrot, Poicephalus robustus (Psittacidae, AVES)

Twenty-two polymorphic microsatellite loci were characterized in the Cape parrot, Poicephalus robustus. Nineteen loci were newly isolated from two Cape parrot genomic libraries, and three loci isolated from other parrot species. Loci were characterized in 40 unrelated captive Cape parrots held by aviculturalists. The loci displayed between two and 24 alleles, with the observed heterozygosities ranging between 0.10 and 0.94. This locus set is suitable for identifying clarifying parentage (parentage exclusion probabilities of P_E1 = 0.0004 and P_E2 = 0.000001). Candidate parents for any Cape parrot individual can now be genotyped to distinguish between individuals, which are truly captive bred and those suspected of being wild-caught birds. Cross-species analysis found up to 31 loci to be polymorphic across 24 additional parrot species tested.     

Microsatellite markers for an invasive tetraploid tree,Chinese tallow (Triadica sebifera)

We present six polymorphic microsatellite loci for Chinese tallow tree (Triadica sebifera, Euphorbiaceae), which is native to East Asia and is an aggressive, invasive species in the southeastern USA, particularly along the Coastal Plain. Microsatellite loci were tested for polymorphism across a total of 79 individuals from populations across the native range of China and in introduced populations of the southeastern USA, California, Hawaii, and Australia. Across these samples, we found a high level of polymorphism, suggesting they will be useful for deducting the introduction history of this invasive species.     

The application of SSRs characterized for grape (Vitis vinifera) to conservation studies in Vitaceae

The use of microsatellite loci developed from a single plant species across a number of related taxa is becoming increasingly widespread. This approach can provide highly informative markers even for species for which microsatellites have not been characterized. As a number of expressed sequence tag (EST)-derived and enrichment-derived microsatellites are available for grape (Vitis vinifera), this study set out to assess transferability of nine such loci across 25 species from five different Vitaceae genera. Intergeneric transfer success in Vitaceae was high (51.1%) and EST-derived loci performed better than enrichment-derived loci. Six loci were further tested across two Australian native species, Cissus hypoglauca and C. sterculiifolia, in order to assess the conservation of microsatellite repeats and their flanking sequences. Polymorphism of these selected loci was successfully tested for each species across a small, isolated rain forest population from northern New South Wales (Australia). Results from this preliminary investigation suggest that it is possible to use grape-derived simple sequence repeats (SSR) loci for population studies on Vitaceae. As Vitaceae are an important component of rain forest flora, the availability of such highly informative loci will be beneficial to future studies aimed at determining the genetic consequences of rain forest fragmentation.     

Isolation and characterization of microsatellite markers for the waratah,Telopea speciosissima (Proteaceae)

Thirteen microsatellite loci were developed from an (AG)‐enriched library using Telopea speciosissima, a widespread species of dry‐sclerophyll forest in New South Wales (NSW, Australia). Genotyping of 30 seeds from one population of T. speciosissima and 15 seeds from one population of the related Telopea aspera (restricted to the Gibraltar Range in northern NSW) was successfully performed. The loci were also tested across seven other related species. The microsatellites will be used to compare population dynamics across a range of taxa representing different distribution patterns.     

Reverse ascertainment bias in microsatellite allelic diversity in owls (Aves, Strigiformes)

A rich source of markers may be overlooked by screening for polymorphism in the source species only. We screened 129 microsatellite loci isolated from the powerful owl (Ninox strenua) against two closely related species; Ninox connivens and Ninox novaeseelandiae. From the screening effort 20 polymorphic markers were isolated, including six loci which were originally discarded as they were monomorphic in the source species. Further cross-species amplification of all 20 loci across species from two families, Strigidae and Tytonidae, revealed unusually high levels of polymorphism within closely related species, and limited success within phylogenetically distant species. Routine screening of multiple species during the marker development phase can yield a wider range of polymorphic markers which can subsequently enhance cross-species amplification attempts.     

Microsatellite primers for the Atlantic coastal killifish,Fundulus heteroclitus,with applicability to related Fundulus species

The mummichog (Fundulus heteroclitus), a common Atlantic coastal killifish, is a model vertebrate species for the study of molecular genetic variation in natural populations and of environmental toxicology. We report the development of a set of 20 microsatellite loci in this species. Average expected heterozygosity across all loci was 0.84 (range: 0.60–0.97), revealing a high level of variability at most loci. A survey of seven additional Fundulus species yielded one or two robust amplification products in over half (63%) of the species–primer combinations tested. Therefore, many of these loci will also prove useful in studies of other members of the genus Fundulus.     

Haldane's rule in an avian system: using cline theory and divergence population genetics to test for differential introgression of mitochondrial, autosomal, and sex-linked loci across the Passerina bunting hybrid zone

Using cline fitting and divergence population genetics, we tested a prediction of Haldane's rule: autosomal alleles should introgress more than z-linked alleles or mitochondrial haplotypes across the Passerina amoena/Passerina cyanea (Aves: Cardinalidae) hybrid zone. We screened 222 individuals collected along a transect in the Great Plains of North America that spans the contact zone for mitochondrial (two genes), autosomal (four loci) and z-linked (two loci) markers. Maximum-likelihood cline widths estimated from the mitochondrial (223 km) and z-linked (309 km) datasets were significantly narrower on average than the autosomal cline widths (466 km). We also found that mean coalescent-based estimates of introgression were larger for the autosomal loci (0.63 genes/generation, scaled to the mutation rate mu) than for both the mitochondrial (0.27) and z-linked loci (0.59). These patterns are consistent with Haldane's rule, but the among-locus variation also suggests many independently segregating loci are required to investigate introgression patterns across the genome. These results provide the first comprehensive comparison of mitochondrial, sex-linked, and autosomal loci across an avian hybrid zone and add to the body of evidence suggesting that sex chromosomes play an important role in the formation and maintenance of reproductive isolation between closely related species.     

Characterization of six microsatellite loci in the African wild silk moth (Gonometa postica,Lasiocampidae)

Six microsatellite markers were developed for the African wild silk moth, Gonometa postica (Lasiocampidae), using an enrichment protocol. The total number of alleles ranged from three to 17 for a sample of 130 individuals across the distribution of the species. Observed levels of heterozygosity ranged from 0.17 to 0.78. Deviation from Hardy–Weinberg equilibrium detected in some loci is probably the result of large interannual population size fluctuations characteristic of this species. No evidence of linkage disequilibrium was detected among loci. These loci will be useful for the inference of demographic processes in a moth species that is of potential economic importance.     

Biogeography and Divergence in Guaiacum sanctum (Zygophyllaceae) Revealed in Chloroplast DNA: Implications for Conservation in the Florida Keys

Guaiacum sanctum (lignumvitae, guayacán) comprises economically important and globally endangered trees endemic to the dry neotropics. These trees were historically over-harvested and now G. sanctum is among the species listed by IUCN and CITES. Guaiacum sanctum was once found throughout the Florida Keys, but anthropogenic habitat fragmentation and exploitation have left only one significant population, on Lignumvitae Key. The ecology of this population is additionally subject to hurricane-mediated effects and an endemic parasite. Genetic profiles were determined for the Lignumvitae and putative source populations of G. sanctum to assess variability and to test biogeographic hypotheses. These data were analyzed by phylogenetic and statistical parsimony analyses. The results were most readily interpreted as indicating historical fragmentation followed by long-term isolation. However, recent dispersal or gene flow could not be entirely excluded. Both types of analyses strongly support a significant genetic divergence between Caribbean and Mexican populations of G. sanctum and also suggest bidirectional dispersal of G. sanctum into Lignumvitae Key from both the Caribbean and Mexico. These results inform the process of restoring G. sanctum in the Keys.     

PERMANENT GENETIC RESOURCES: Microsatellite markers for the threatened Bliss Rapids snail (Taylorconcha serpenticola) and cross-amplification in its congener, T. insperata

We developed and tested microsatellite markers to investigate population structure of a threatened North American freshwater gastropod, Taylorconcha serpenticola. Of the 21 primer pairs that were evaluated, 11 were readily optimized and scored, providing amplification of 12 loci that were screened for 820 specimens from 29 populations. The number of alleles across 11 of these polymorphic loci ranged from three to 20 and the observed heterozygosity varied from 0.0061 to 0.7561. All loci yielded suitable amplification products in the second species of Taylorconcha (T. insperata) and three proved to be diagnostic for these congeners, demonstrating that these markers are also useful for species identification studies.     

Evidence for evolutionary change associated with the recent range expansion of the British butterfly, Aricia agestis, in response to climate change

Poleward range expansions are widespread responses to recent climate change and are crucial for the future persistence of many species. However, evolutionary change in traits such as colonization history and habitat preference may also be necessary to track environmental change across a fragmented landscape. Understanding the likelihood and speed of such adaptive change is important in determining the rate of species extinction with ongoing climate change. We conducted an amplified fragment length polymorphism (AFLP)‐based genome scan across the recently expanded UK range of the Brown Argus butterfly, Aricia agestis, and used outlier‐based (DFDIST and BayeScan) and association‐based (Isolation‐By‐Adaptation) statistical approaches to identify signatures of evolutionary change associated with range expansion and habitat use. We present evidence for (i) limited effects of range expansion on population genetic structure and (ii) strong signatures of selection at approximately 5% AFLP loci associated with both the poleward range expansion of A. agestis and differences in habitat use across long‐established and recently colonized sites. Patterns of allele frequency variation at these candidate loci suggest that adaptation to new habitats at the range margin has involved selection on genetic variation in habitat use found across the long‐established part of the range. Our results suggest that evolutionary change is likely to affect species’ responses to climate change and that genetic variation in ecological traits across species’ distributions should be maximized to facilitate range shifts across a fragmented landscape, particularly in species that show strong associations with particular habitats.