Intraspecific Diversity of Short-Legged Horned Toad (Boulenophrys brachykolos) in Hong Kong: Identification of a Distinct Conservation Unit on Lantau Island

A genetic evaluation of conservation units and four decades of translocation history for <i>Banksia cuneata</i> , an iconic threatened species in a biodiversity hotspot

Conservation biologists often apply evolutionarily defensible definitions of conservation units, such as evolutionarily significant units (ESU; Moritz 1994, 1995; Vogler & DeSalle 1994), when assessing the conservation status of populations (Legge et al. 1996; Britten et al. 1997; Pichler et al. 1998; Waits et al. 1998; Zhu et al. 1998; Roman et al. 1999). Conversely, taxonomists often do not explicitly invoke any definition when delineating their fundamental units, species. For example, only 4 of 74 species descriptions (fishes, amphibians, and reptiles) published in Copeia since 1995 identify an underlying species definition. We can only assume, based on the morphological emphasis, that a morphological species concept is applied in most of these instances. Three problems can result from taxonomic practices that delineate species without an operational evolutionary framework. First, the characteristics of species (e.g., reproductively isolated arrays or monophyletic assemblages) are not adequately defined to prevent these evolutionary units from becoming simple arrays of individuals that are distinct along one or a few axes (e.g., families). Second, a fundamental partition (diagnostic character) frequently frames analyses of character variation in subsequent studies, an operational flaw in taxonomic practice (Wilson & Brown 1953) from which population geneticists are not immune. Third, conflicting patterns of distinctiveness among individual characters lead to taxonomic confusion and inevitable controversy over what constitutes a good characteristic for taxon-level descriptions. These problems contribute to taxonomic and conservation controversies such as that outlined by Karl and Bowen (this issue) that consume limited conservation resources. Examining variation among genetically independent characters for common patterns (character concordance) might reduce taxonomic controversy by providing an evolutionary framework within which character variation can be objectively evaluated. The black-green turtle debate illustrates the problem of taxonomy without an evolutionary framework, the inevitable controversy that ensues, and the advantage of a character concordance approach. Black turtles were first recognized as taxonomically distinct because they are not green but nonetheless resemble green turtles in other attributes (Bocourt 1868). Under many species concepts, species are distinct units, but distinctness is a relative assessment that can apply to a variety of hierarchical levels, including individuals (Vogler & DeSalle 1994). Also, arrays of organisms can be distinct for reasons other than a shared history of divergence, for example, when the phenotype is largely determined environmentally. When our expectation is that species constitute distinctive arrays of individuals and our focus is a single trait-color, for example-we risk delineating nonevolutionary units as species.

Anthropogenic global change is impacting the evolutionary potential of biodiversity in ways that have been difficult to predict. Distinct evolutionary units within species may respond differently to the same environmental trends, reflecting unique geography, ecology, adaptation, or drift. Least shrews (Cryptotis parvus group) have a widespread distribution across North America, yet systematic relationships and ongoing evolutionary processes remain unresolved. Westernmost peripheral populations have been prioritized for conservation, but little is known of their evolutionary histories or population trajectories. The broad range of this group of species is coincident with many other temperate taxa, presenting a hypothesis that diversification of least shrews follows a repeated process through the Pleistocene, leading to regionally diagnosable conservation units. We use genomic data and niche modeling to delimit species and conservation units of least shrews. Our results show that least shrews warrant recognition as multiple distinct species, along with geographically discrete infraspecific lineages of C. parvus (sensu stricto). Western peripheral populations are evolutionarily distinct based on nuclear, but not mitochondrial data, possibly reflecting mitochondrial capture during the last glacial phase. This population represents a relict conservation unit, consistent with both an "adaptive unit" and "management unit" based on non-neutral and neutral divergence, respectively. Hindcast niche modeling supports growing evidence for a shared process of diversification among co-distributed biota, and forecast modeling suggests continued future loss of suitable environmental niche in peripheral regions. Given mito-nuclear discordance among samples of parapatric lineages, future environmental perturbation may continue to impact the genomic integrity of important conservation units, making ecological and genomic monitoring a critical need.

Matschie’s tree kangaroo (Dendrolagus matschiei), New Guinea pademelon (Thylogale browni), and small dorcopsis (Dorcopsulus vanheurni) are sympatric macropodid taxa, of conservation concern, that inhabit the Yopno–Urawa–Som (YUS) Conservation Area on the Huon Peninsula, Papua New Guinea. We sequenced three partial mitochondrial DNA (mtDNA) genes from the three taxa to (i) investigate network structure; and (ii) identify conservation units within the YUS Conservation Area. All three taxa displayed a similar pattern in the spatial distribution of their mtDNA haplotypes and the Urawa and Som rivers on the Huon may have acted as a barrier to maternal gene flow. Matschie’s tree kangaroo and New Guinea pademelon within the YUS Conservation Area should be managed as single conservation units because mtDNA nucleotides were not fixed for a given geographic area. However, two distinct conservation units were identified for small dorcopsis from the two different mountain ranges within the YUS Conservation Area.

The Ogasawara Islands, one of the UNESCO World Natural Heritage Site located about 1000 km south of Japan’s main island, harbor numerous endemic species, many of which are as endangered. One of the endemic plant species, Lobelia boninensis, found in the Mukojima, Chichijima, and Hahajima archipelagoes, is endangered due to predation. As part of conservation efforts, translocation is now underway, especially on Chichijima. However, we lack essential information, such as the genetic population structure, to develop appropriate translocation strategies for both wild and planted individuals. Here, we aimed to identify the conservation units and the origin of planted individuals by estimating the genetic population structure and phylogenetic relationships across all habitats of this species. We identified two distinct genetic clusters, indicating genetic differentiation between the northern and southern populations. The genetic population components detected at an isolated site on Chichijima showed a mixture of these distinct clusters, probably due to hybridization. The transplanted individuals in Chichijima were found to have originated from a population in Hahajima. These results suggest the presence of two distinct conservation units. Furthermore, the current translocation strategy poses a risk of genetic contamination between these units, highlighting the need for revised conservation management practices.

Extreme neutral genetic and morphological divergence supports classification of Adriatic three-spined stickleback (Gasterosteus aculeatus) populations as distinct conservation units

The objectives of this study were to describe and evaluate potential drivers of genetic structure in Canadian breeding populations of the Ovenbird, Seiurus aurocapilla. We performed genetic analyses on feather samples of individuals from six study sites using nuclear microsatellites. We also assessed species identity and population genetic structure of quill mites (Acariformes, Syringophilidae). For male Ovenbirds breeding in three study sites, we collected light‐level geolocator data to document migratory paths and identify the wintering grounds. We also generated paleohindcast projections from bioclimatic models of Ovenbird distribution to identify potential refugia during the last glacial maximum (LGM, 21,000 years before present) as a factor explaining population genetic structure. Birds breeding in the Cypress Hills (Alberta/Saskatchewan) may be considered a distinct genetic unit, but there was no evidence for genetic differentiation among any other populations. We found relatively strong migratory connectivity in both western and eastern populations, but some evidence of mixing among populations on the wintering grounds. There was also little genetic variation among syringophilid mites from the different Ovenbird populations. These results are consistent with paleohindcast distribution predictions derived from two different global climate models indicating a continuous single LGM refugium, with the possibility of two refugia. Our results suggest that Ovenbird populations breeding in boreal and hemiboreal regions are panmictic, whereas the population breeding in Cypress Hills should be considered a distinct management unit.

The radiated tortoise (Geochelone radiata) is an endangered species endemic to Madagascar. It inhabits the semiarid spiny forest of the southern part of the island, an ecosystem heavily affected by habitat destruction. Furthermore, illegal harvesting greatly threatens this species. The main objective of our study was to acquire better knowledge of its genetic structure, in order to take appropriate management decisions concerning, for instance, the reintroduction of confiscated individuals. Our hypothesis was that rivers represent effective barriers to tortoise dispersal despite the fact that they are dry most of the year. We used 13 polymorphic microsatellite markers to compare samples from six populations across the range of the species. All analyses (Fisher’s exact tests, FST values, AMOVA) indicated that the radiated tortoise exhibits moderate levels of genetic structure throughout its range. In addition, we used a multiple regression approach that revealed the importance of rivers to explain the observed structure. This analysis supported the role of the Menarandra and Manambovo Rivers as major barriers to the dispersal of most radiated tortoises, but Markov chain Monte Carlo simulations revealed that low levels of recurrent gene flow may explain why FST values were not higher. We identified three distinct conservation units with relatively high assignments rates (87%), which should be valuable for the management of the species. This is the first study to report the genetic structure of a species sampled throughout the Malagasy spiny forest.

In addition to the usual suite of human-related threats to persistence (habitat destruction and fragmentation, competition and exotic diseases from livestock, poaching), the conservation of endangered wild sheep and goats (Ovis and Capra spp.) is hampered by a limited knowledge of their taxonomy. Taxonomic knowledge is important because it allows the preservation of local adaptations, avoidance of hybridization and, for reintroductions, the re-establishment of the right species in the right places. The taxonomy of wild sheep and goats, especially in Africa and Asia, is complicated by intergradation and hybridization of taxa, limited data owing to poor accessibility to much of their remote mountainous habitat, and contrasting results of molecular and morphological studies. Of all wild goats, the least known and the most endangered is the Walia ibex Caprawalie, restricted since historic times to the Siemen Mountains of Ethiopia, where a current population of about 450 uses 95 km2 of rugged high-elevation habitat. Although these ibex look very different from Nubian ibex Capra nubiana found in deserts around the Red Sea, they are likely related to them, and their status as a distinct species has been questioned. Gebremedhin et al. (2009) used DNA extracted from fecal samples and information on the physical and climatic characteristics of habitat used by both Walia and Nubian ibex to conclude that there are considerable genetic and substantial ecological differences between these taxa. Those differences justify the treatment of Walia ibex as a separate and valuable conservation and taxonomic unit. In other words, Walia ibex are a ‘good species.’ Unlike the desert-adapted Nubian ibex, the Walia ibex lives in a cold, high-elevation mountainous environment with substantial precipitation. Even though the two groups probably diverged less than a million year ago, they are now very different. As the authors point out, the estimated time since these two ibex became separated is likely three times as long as the apparent divergence time between polar and brown bears (Ursus maritimus and Ursus arctos). Clearly, morphological differences and ecological adaptations are not necessarily a simple function of time or of genetic divergence: this is an extremely important point for both ecology and conservation. The main key to taxonomic divergence and therefore to speciation is not time, but differences in local selective pressures. Those different selective pressures lead to different adaptations, and preserving local adaptations must be a major goal of conservation. That means that we cannot simply quantify genetic differences along some chunk of DNA and always expect those differences to closely match either ecological specialization or conservation value. Both taxonomy and conservation require a holistic approach, considering genetics, morphology, ecology and, above all, evidence of local adaptation. The key point here is not whether Walia ibex either looks different from Nubian ibex or whether the Fst between the two is large or small – the point is that Walia ibex evolved adaptations to the highlands of Ethiopia and Nubian ibex are adapted to the desert! Pretending that weak genetic differentiation is relevant to conservation in this case is like arguing that polar and brown bears are not different. Importantly, the research by Gebremedhin and colleagues also identifies potential suitable habitat for Walia ibex outside its present range. These areas are possible candidates for introduction or reintroduction. Unfortunately, there is currently no information available about the former distribution of Walia ibex outside the Siemen Mountains, and the study also concluded that this species' decline may have been ongoing for a very long time. Knowledge about potential habitat, however, is very valuable for the conservation of this species, as the establishment of a separate population may serve as an insurance policy against any catastrophe that may affect the Siemen population. On the other hand, habitat analyses cannot by themselves identify all threats to a population, and before any introduction or reintroduction is attempted, information is required about competition from livestock, risks of poaching and other possible threats that may be faced by a new population. Those considerations are particularly important for a species that is already at risk because of low numbers, very small distribution and, as Gebremedhin and colleagues report, low genetic variability. Inevitably, any newly established population would have less genetic variability lower than the source. However, because the study found that there is substantial suitable habitat within the Siemen Mountains not currently used by ibex, it may be possible to establish new populations with some natural gene flow with the existing population. In the early 19th century, there were perhaps fewer than 100 Alpine ibex Capra ibex, all in the Gran Paradiso area of Italy. Tens of thousands are alive today and the ibex is again widely distributed in the Alps. That remarkable success was achieved through reintroductions, control of poaching and habitat protection. The news that there is substantial remaining habitat apparently available for Walia ibex gives hope that reintroductions and effective protection may see this species flourish in the future.

Species are the most commonly recognised unit for conservation management, yet significant variation can exist below the level of taxonomic recognition and there is a lack of consensus around how a species might be defined. This definition has particular relevance when species designations are used to apportion conservation effort and when definitions might be made through legislation. Here, we use microsatellite DNA analyses to test the proposition that the last remaining populations of the endangered grassland earless dragon (Tympanocryptis pinguicolla) harbour substantial cryptic genetic variation. Our study provides strong evidence that long historical isolation and the recent impacts of urbanization, have led to genetic differentiation in microsatellite DNA allele frequencies and high numbers of private alleles among three genetic clusters. This differentiation is partially concordant with previous mitochondrial DNA analyses, which show the two regions (Canberra and Monaro) where this species exists, to be reciprocally monophyletic, but differs through the identification of a third genetic cluster that splits a northern Canberra cluster from that of southern Canberra. Our data also identify a stark contrast in population genetic structure between clusters such that high levels of genetic structure are evident in the highly urbanised Canberra region but not in the largely rural Monaro region. We conclude that this species, like many reptiles, harbours considerable cryptic variation and currently comprises three distinct and discrete units. These units could be classified as separate species for the purpose of conservation under the relevant Australian and international Acts drawing management appropriate to that status.

Conservation programs for threatened species are greatly benefiting from genetic data, for their power in providing knowledge of dispersal/gene flow across fragmented landscapes and for identifying populations of high conservation value. The endangered southern brown bandicoot (Isoodon obesulus obesulus) has a disjunct distribution range in South Australia, raising the possibility that populations of the subspecies may represent distinct conservation units. In the current study, we used a combination of 14 microsatellite and two mitochondrial sequence markers to investigate the phylogeography and population structure of I. o. obesulus in South Australia and south-western Victoria, with the aim of identifying any potential evolutionarily significant units and management units relevant to conservation management. Our phylogenetic/population analyses supported the presence of two distinct evolutionary lineages of I. o. obesulus. The first lineage comprised individuals from the Mount Lofty Ranges, Fleurieu Peninsula and Kangaroo Island. A second lineage comprised individuals from the south-east of South Australia and south-western Victoria. We propose that these two lineages represent distinct evolutionarily significant units and should be managed separately for conservation purposes. The findings also raise significant issues for the national conservation status of I. o. obesulus and suggest that the current subspecies classification needs further investigation.

Using phylogeography to define conservation priorities: The case of narrow endemic plants in the Mediterranean Basin hotspot

The spatial distribution of a species’ genetic diversity can provide insights into underlying evolutionary, ecological and environmental processes, and can contribute information towards the delineation of conservation units. The Knysna seahorse, Hippocampus capensis, is endangered and occurs in only three estuaries on the warm-temperate south coast of South Africa: Knsyna, Keurbooms and Swartvlei. Population sizes in the latter two estuaries have been very small for a prolonged period of time, and the populations residing in them may thus benefit from translocations as a means of increasing population sizes and possibly also genetic diversity. However, information on whether these three estuaries constitute distinct conservation units that warrant separate management is presently lacking. Here, we used genetic information from mitochondrial (control region) and nuclear microsatellite loci to assess the genetic diversity and spatial structure across the three estuaries, and also whether translocations should be included in the management plan for the Knysna seahorse. Although each population had a unique combination of alleles, and clustering methods identified the Swartvlei Estuary as being distinct from the others, levels of genetic admixture were high, and there was no evidence for reciprocal monophyly that would indicate that each estuary has a unique demographic history. On these grounds, we suggest recognising the three populations as a single evolutionarily significant unit (ESU), and encourage translocations between them to ensure the species’ long-term survival.

The genetic variation of the critically endangered Corfu killifish (Valencia letourneuxi), an endemic freshwater fish species of the western Balkans, was assessed for nine populations sampled in eight water systems in western continental Greece, the Peloponnese and the Ionian Island of Corfu, using mitochondrial and microsatellite markers. The analyses were based on data from three mtDNA regions (D-loop, COI and 16S rRNA sequences) and 14 microsatellite loci. Samples from the congeneric species Valencia hispanica and the phylogenetically closely related species Aphanius fasciatus were also used in the study as outgroups. Both the mitochondrial and the microsatellite analyses revealed three distinct population groupings associated with the geographical distribution of the populations: one southern group occupying rivers draining to the Patraikos Gulf, the second one including the populations flowing into the Amvrakikos Gulf and the third, more northern group, including the other populations from rivers in Corfu Island and Epirus flowing into the Ionian Sea. Within these groupings there is limited genetic differentiation between populations; in addition, there is reduced intrapopulation genetic variation, evidenced by low heterozygosity values, number of alleles and haplotype diversity. In terms of taxonomic implications and appropriate management actions for conservation, our data suggest that the major population groups should be regarded at least as three distinct conservation units (CUs), with translocation and restocking actions to take place only within the geographical range of the CU concerned. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111, 334–349.

The genus Steindachneridion, which includes large-sized freshwater pimelodid species, is endemic to the southeastern coastal drainages of South America, specifically the Paraná River and Uruguay River basins. In this study, genetic analyses of mitochondrial DNA (mtDNA) D-loop were conducted on four species within this genus across their respective distributions: Steindachneridion scriptum (from the Tibagi and Uruguay rivers), S. melanodermatum (from the Iguaçu River), S. doceanum (from the Doce River), and S. parahybae (from the Paraíba do Sul River). Zungaro zungaro and Brachyplatystoma rousseauxii were employed as outgroups, and the topology was inferred using Bayesian Inference (BI) and maximum likelihood (ML) phylogenetic reconstruction techniques. Additionally, the sequences were analyzed to assess genetic diversity levels. In contrast to the remaining species, which exhibited distinct species-specific clades, our data suggests that S. scriptum formed two sister clades, potentially representing distinct operational taxonomic units. Novel haplotypes were identified for each of the four species, further supporting the conclusions derived from the phylogenetic analysis. Overall, Steindachneridion species displayed high haplotype diversity paired with low nucleotide diversity, indicating a demographic expansion event after reduced effective population size. Nevertheless, genetic structure indexes were notably high. These findings suggest that the genetic diversity within these species may be underestimated, which has implications for both taxonomic classification and biological conservation strategies. In conclusion, the study of genetic diversity in four Steindachneridion species has revealed distinct molecular operational taxonomic units (MOTUs), which highlights the necessity for conservation efforts. The detection of new haplotypes and intraspecific variability emphasizes the urgency of implementing systematic conservation measures in the face of looming extinction threats.