Revisiting the radiation of Gazella arabica on the Arabian Peninsula and testing the suitability of captive breeding stock for reintroduction, using mitochondrial and nuclear markers.

Today, the Arabian gazelle (G. arabica) occurs only in small, scattered populations on the Arabian Peninsula and is classified as 'vulnerable', due to intensive hunting and competition with livestock. The taxonomy of this threatened species is still under debate, hampering conservation efforts while ex-situ breeding programs could be an appropriate conservation measure to prevent the species from going extinct. In our study, we attempted to elucidate the radiation of G. arabica on the Arabian Peninsula, and to ask whether the population genetic structure allows to distinguish between discrete conservation units. We used mitochondrial markers, microsatellite markers, and three intron markers to identify conservation units, to match them with genotypes found in the captive breeding stock held in Saudi Arabia, and to ensure that genotype diversity of potential founder individuals corresponds to that prevailing at targeted reintroduction sites. The sequence divergence was low among nuclear and mitochondrial markers, with gazelles originating from the north of the Arabian Peninsula showing the largest diversity, while south-western and eastern populations showed a decreased diversity. A haplotype network based on the relatively heterogeneous cytochrome b gene found no signs of a prolonged separate evolutionary history of any investigated mainland population, suggesting limitations of gene-flow after the colonization of the Arabian Peninsula leading to a founder effect-like distribution of mitochondrial haplotypes. The ex-situ breeding population held in Saudi Arabia showed a good haplotype diversity, underlining its general suitability for reintroductions. However, it is recommended that genetic data of founders should be assessed prior to future reintroduction.

Gazella arabica dareshurii: a remarkable relict population on Farur Island, Iran.

BACKGROUND: The islands in the Persian Gulf are home to several species of gazelles, i.e., Gazella bennettii, G. subgutturosa, and a new subspecies of Mountain gazelles which was discovered on Farur Island and described for the first time in 1993 as Gazella gazella dareshurii. Later, phylogenetic analyses showed that the Mountain gazelles consist of two species: G. gazella and G. arabica. As the Farur gazelles are more closely related to the Arabian forms of the Mountain gazelles, this subspecies is regarded to be G. arabica dareshurii. Until now, the origin of this subspecies has been an enigma. RESULTS: Here, we used mitochondrial cyt b, two nuclear introns (CHD2 and ZNF618), and morphological data to address this question by investigating the taxonomic position of the Farur gazelles. The results show that this population is monophyletic and split from other G. arabica populations probably 10,000 BP. CONCLUSIONS: It is a natural relict population that was trapped on the island due to the rising sea levels of the Persian Gulf after the Last Glacial Maximum. Intermittent drought and flooding are suggested to be the main factors balancing population growth in the absence of natural predators on this monsoon-influenced island. Conservation actions should focus on preserving the natural situation of the island (cease introducing mesquite tree and other invasive species, stop building new construction and roads, and caution in providing water sources and forage), and possibly introducing individuals to other islands (not inhabited by gazelles) or to fenced areas on the Iranian mainland (strictly isolated from other gazelle populations) when the population reaches the carrying capacity of the island.

Repeated hybridization of two closely related gazelle species (Gazella bennettii and Gazella subgutturosa) in central Iran.

Interspecific hybridization increasingly occurs in the course of anthropogenic actions, such as species translocations and introductions, and habitat modifications or occurs in sympatric species due to the shortage of conspecific mates. Compared with anthropogenically caused hybridization, natural hybridization is more difficult to prove, but both play an important role in conservation. In this study, we detected hybridization of two gazelle sister species, Gazella bennettii (adapted to dry areas) and Gazella subgutturosa (adapted to open plains), in five habitat areas, where G. bennettii naturally occur in central Iran. The hybrids have a nuclear genomic identity (based on two introns), habitat preference, and phenotype of G. bennettii, but the mitochondrial identity (based on cyt b) of G. subgutturosa. We suggest that natural hybridization of female G. subgutturosa and male G. bennettii happened twice in central Iran in prehistoric times, based on the haplotype pattern that we found. However, we found indications of recent hybridization between both species under special circumstances, for example, in breeding centers, due to translocations, or in areas of sympatry due to the shortage of conspecific mates. Therefore, these two species must be kept separately in the breeding centers, and introduction of one of them into the habitat of the other must be strictly avoided.

Diversification and subspecies patterning of the goitered gazelle (Gazella subgutturosa) in Iran.

Goitered gazelles, Gazella subgutturosa, exist in arid and semiarid regions of Asia from the Middle to the Far East. Although large populations were present over a vast area until recently, a decline of the population as a result of hunting, poaching, and habitat loss led to the IUCN classification of G. subgutturosa as "vulnerable." We examined genetic diversity, structure, and phylogeny of G. subgutturosa using mitochondrial cytochrome b sequences from 18 geographically distant populations in Iran. The median-joining network of cyt b haplotypes indicated that three clades of goitered gazelles can be distinguished: a Middle Eastern clade west of the Zagros Mountains (and connected to populations in Turkey and Iraq), a Central Iranian clade (with connection to Azerbaijan), and an Asiatic clade in northeastern Iran (with connection to Turkmenistan, Uzbekistan, and other Asian countries as far as northeastern China and Mongolia). Based on our results, we argue that Iran is the center of diversification of goitered gazelles, due to the presence of large mountain ranges and deserts that lead to the separation of populations. In accordance with previous morphological studies, we identified the Asiatic clade as the subspecies G. s. yarkandensis, and the other two clades as the nominate form G. s. subgutturosa. The new genetic information for goitered gazelles in Iran provides the basis for future national conservation programs of this species.

Population genetics of the European rabbit along a rural-to-urban gradient.

The European rabbit (Oryctolagus cuniculus) is declining in large parts of Europe but populations in some German cities remained so far unaffected by this decline. The question arises of how urbanization affects patterns of population genetic variation and differentiation in German rabbit populations, as urban habitat fragmentation may result in altered meta-population dynamics. To address this question, we used microsatellite markers to genotype rabbit populations occurring along a rural-to-urban gradient in and around the city of Frankfurt, Germany. We found no effect of urbanization on allelic richness. However, the observed heterozygosity was significantly higher in urban than rural populations and also the inbreeding coefficients were lower, most likely reflecting the small population sizes and possibly on-going loss of genetic diversity in structurally impoverished rural areas. Global FST and G'ST-values suggest moderate but significant differentiation between populations. Multiple matrix regression with randomization ascribed this differentiation to isolation-by-environment rather than isolation-by-distance. Analyses of migration rates revealed asymmetrical gene flow, which was higher from rural into urban populations than vice versa and may again reflect intensified agricultural land-use practices in rural areas. We discuss that populations inhabiting urban areas will likely play an important role in the future distribution of European rabbits.

Extremophile Poeciliidae: multivariate insights into the complexity of speciation along replicated ecological gradients.

BACKGROUND: Replicate population pairs that diverge in response to similar selective regimes allow for an investigation of (a) whether phenotypic traits diverge in a similar and predictable fashion, (b) whether there is gradual variation in phenotypic divergence reflecting variation in the strength of natural selection among populations, (c) whether the extent of this divergence is correlated between multiple character suites (i.e., concerted evolution), and (d) whether gradual variation in phenotypic divergence predicts the degree of reproductive isolation, pointing towards a role for adaptation as a driver of (ecological) speciation. Here, we use poeciliid fishes of the genera Gambusia and Poecilia that have repeatedly evolved extremophile lineages able to tolerate high and sustained levels of toxic hydrogen sulfide (H2S) to answer these questions. RESULTS: We investigated evolutionary divergence in response to H2S in Gambusia spp. (and to a lesser extent Poecilia spp.) using a multivariate approach considering the interplay of life history, body shape, and population genetics (nuclear miscrosatellites to infer population genetic differentiation as a proxy for reproductive isolation). We uncovered both shared and unique patterns of evolution: most extremophile Gambusia predictably evolved larger heads and offspring size, matching a priori predictions for adaptation to sulfidic waters, while variation in adult life histories was idiosyncratic. When investigating patterns for both genera (Gambusia and Poecilia), we found that divergence in offspring-related life histories and body shape were positively correlated across populations, but evidence for individual-level associations between the two character suites was limited, suggesting that genetic linkage, developmental interdependencies, or pleiotropic effects do not explain patterns of concerted evolution. We further found that phenotypic divergence was positively correlated with both environmental H2S-concentration and neutral genetic differentiation (a proxy for gene flow). CONCLUSIONS: Our results suggest that higher toxicity exerts stronger selection, and that divergent selection appears to constrain gene flow, supporting a scenario of ecological speciation. Nonetheless, progress toward ecological speciation was variable, partially reflecting variation in the strength of divergent selection, highlighting the complexity of selective regimes even in natural systems that are seemingly governed by a single, strong selective agent.

Data on phylogenetic analyses of gazelles (genus Gazella) based on mitochondrial and nuclear intron markers.

The data provided is related to the article "Phylogenetic analyses of gazelles reveal repeated transitions of key ecological traits and provide novel insights into the origin of the genus Gazella" [1]. The data is based on 48 tissue samples of all nine extant species of the genus Gazella, namely Gazella gazella, Gazella arabica, Gazella bennettii, Gazella cuvieri, Gazella dorcas, Gazella leptoceros, Gazella marica, Gazella spekei, and Gazella subgutturosa and four related taxa (Saiga tatarica, Antidorcas marsupialis, Antilope cervicapra and Eudorcas rufifrons). It comprises alignments of sequences of a cytochrome b data set and of six nuclear intron markers. For the latter new primers were designed based on cattle and sheep genomes. Based on these alignments phylogenetic trees were inferred using Bayesian Inference and Maximum Likelihood methods. Furthermore, ancestral character states (inferred with BayesTraits 1.0) and ancestral ranges based on a Dispersal-Extinction-Cladogenesis model were estimated and results׳ files were stored within this article.

Phylogenetic analyses of gazelles reveal repeated transitions of key ecological traits and provide novel insights into the origin of the genus Gazella.

African bovids are a famous example of a taxonomic group in which the correlated evolution of body size, feeding mode, gregariousness, and social organization in relation to the preferred habitat type has been investigated. A continuum has been described ranging from small-bodied, sedentary, solitary or socially monogamous, forest- or bush-dwelling, browsing species that seek shelter from predation in dense vegetation, to large-bodied, migratory, highly gregarious, grazing taxa inhabiting open savannahs and relying on flight or group-defense behaviors when facing predators. Here, we examined a geographically widespread clade within the Bovidae (the genus Gazella) that shows minimal interspecific variation in body size and asked if we could still uncover correlated changes of key ecological and behavioral traits during repeated transitions from open-land to mountain-dwelling. Our study used a multi-locus phylogeny (based on sequence variation of Cytb and six nuclear intron markers) of all extant members of the genus Gazella to infer evolutionary patterns of key ecological and behavioral traits and to estimate ancestral character states using Bayesian inference. At the base of the Gazella-phylogeny, open plains were inferred as the most likely habitat type, and three independent transitions toward mountain-dwelling were uncovered. Those shifts coincided with shifts from migratory to sedentary lifestyles. Character estimation for group size was largely congruent with movement patterns in that species forming large groups tended to be migratory, while small group size was correlated with a sedentary lifestyle. Evolutionary patterns of two other conspicuous traits (twinning ability vs. exclusive singleton births and hornless vs. horned females) did not follow this trend in the Gazella-phylogeny. Furthermore, we inferred the genus Gazella to have emerged in the Late Miocene to Pliocene (10-3Mya), and estimating ancestral ranges based on a Dispersal-Extinction-Cladogenesis model found the Middle East to be the most likely origin of the genus.

Gene expression patterns underlying parasite-induced alterations in host behaviour and life history.

Many parasites manipulate their hosts' phenotype. In particular, parasites with complex life cycles take control of their intermediate hosts' behaviour and life history to increase transmission to their definitive host. The proximate mechanisms underlying these parasite-induced alterations are poorly understood. The cestode Anomotaenia brevis affects the behaviour, life history and morphology of parasitized Temnothorax nylanderi ants and indirectly of their unparasitized nestmates. To gain insights on how parasites alter host phenotypes, we contrast brain gene expression patterns of T. nylanderi workers parasitized with the cestode, their unparasitized nestmates and unparasitized workers from unparasitized colonies. Over 400 differentially expressed genes between the three groups were identified, with most uniquely expressed genes detected in parasitized workers. Among these are genes that can be linked to the increased lifespan of parasitized workers. Furthermore, many muscle (functionality) genes are downregulated in these workers, potentially causing the observed muscular deformations and their inactive behaviour. Alterations in lifespan and activity could be adaptive for the parasite by increasing the likelihood that infected workers residing in acorns are eaten by their definitive host, a woodpecker. Our transcriptome analysis reveals numerous gene expression changes in parasitized workers and their uninfected nestmates and indicates possible routes of parasite manipulation. Although causality still needs to be established, parasite-induced alterations in lifespan and host behaviour appear to be partly explained by morphological muscle atrophy instead of central nervous system interference, which is often the core of behavioural regulation. Results of this study will shed light upon the molecular basis of antagonistic species interactions.

Parallel evolution of cox genes in H2S-tolerant fish as key adaptation to a toxic environment.

Populations that repeatedly adapt to the same environmental stressor offer a unique opportunity to study adaptation, especially if there are a priori predictions about the genetic basis underlying phenotypic evolution. Hydrogen sulphide (H2S) blocks the cytochrome-c oxidase complex (COX), predicting the evolution of decreased H2S susceptibility of the COX in three populations in the Poecilia mexicana complex that have colonized H2S-containing springs. Here, we demonstrate that decreased H2S susceptibility of COX evolved in parallel in two sulphide lineages, as evidenced by shared amino acid substitutions in cox1 and cox3 genes. One of the shared substitutions likely triggers conformational changes in COX1 blocking the access of H2S. In a third sulphide population, we detect no decreased H2S susceptibility of COX, suggesting that H2S resistance is achieved through another mechanism. Our study thus demonstrates that even closely related lineages follow both parallel and disparate molecular evolutionary paths to adaptation in response to the same selection pressure.

Utility of island populations in re-introduction programmes--relationships between Arabian gazelles (Gazella arabica) from the Farasan Archipelago and endangered mainland populations.

Understanding local adaptation and population differentiation is vital to the success of re-introduction initiatives. As other mammals living on islands, Arabian gazelles (G. arabica) show reduced body size on the Farasan archipelago, which we corroborated in this study through morphometric analyses of skulls. In the light of the steep population decline on the Arabian Peninsula ­ but stable population development on the archipelago ­ we tested the potential suitability of Farasan gazelles as a source for re-introductions on the mainland. We therefore investigated genetic differentiation between Farasan and mainland populations using eleven nuclear microsatellite loci and detected a distinct genetic cluster exclusively present on the archipelago, which we inferred to be separated from the mainland cluster for less than 2000 years. About 30% of sampled individuals from Farasan Islands showed assignment to a mainland cluster with signs of ongoing introgression. Analyses using the isolation-with-migration model confirmed recent (probably human-induced) bidirectional exchange of gazelles between mainland and island populations. Hence, the surprisingly uniform island dwarfism most likely reflects phenotypic plasticity, that is, altered morphology as a direct consequence of harsh environmental conditions and resource limitation on the archipelago. Should a further decline of Arabian gazelles on the mainland necessitate restocking in the future, Farasan gazelles may thus become an additional source for captive breeding programmes.

Genetic differentiation and selection against migrants in evolutionarily replicated extreme environments.

We investigated mechanisms of reproductive isolation in livebearing fishes (genus Poecilia) inhabiting sulfidic and nonsulfidic habitats in three replicate river drainages. Although sulfide spring fish convergently evolved divergent phenotypes, it was unclear if mechanisms of reproductive isolation also evolved convergently. Using microsatellites, we found strongly reduced gene flow between adjacent populations from different habitat types, suggesting that local adaptation to sulfidic habitats repeatedly caused the emergence of reproductive isolation. Reciprocal translocation experiments indicate strong selection against immigrants into sulfidic waters, but also variation among drainages in the strength of selection against immigrants into nonsulfidic waters. Mate choice experiments revealed the evolution of assortative mating preferences in females from nonsulfidic but not from sulfidic habitats. The inferred strength of sexual selection against immigrants (RI(s)) was negatively correlated with the strength of natural selection (RI(m)), a pattern that could be attributed to reinforcement, whereby natural selection strengthens behavioral isolation due to reduced hybrid fitness. Overall, reproductive isolation and genetic differentiation appear to be replicated and direct consequences of local adaptation to sulfide spring environments, but the relative contributions of different mechanisms of reproductive isolation vary across these evolutionarily independent replicates, highlighting both convergent and nonconvergent evolutionary trajectories of populations in each drainage.

The rediscovery of a long described species reveals additional complexity in speciation patterns of poeciliid fishes in sulfide springs.

The process of ecological speciation drives the evolution of locally adapted and reproductively isolated populations in response to divergent natural selection. In Southern Mexico, several lineages of the freshwater fish species of the genus Poecilia have independently colonized toxic, hydrogen sulfide-rich springs. Even though ecological speciation processes are increasingly well understood in this system, aligning the taxonomy of these fish with evolutionary processes has lagged behind. While some sulfide spring populations are classified as ecotypes of Poecilia mexicana, others, like P. sulphuraria, have been described as highly endemic species. Our study particularly focused on elucidating the taxonomy of the long described sulfide spring endemic, Poecilia thermalis Steindachner 1863, and investigates if similar evolutionary patterns of phenotypic trait divergence and reproductive isolation are present as observed in other sulfidic species of Poecilia. We applied a geometric morphometric approach to assess body shape similarity to other sulfidic and non-sulfidic fish of the genus Poecilia. We also conducted phylogenetic and population genetic analyses to establish the phylogenetic relationships of P. thermalis and used a population genetic approach to determine levels of gene flow among Poecilia from sulfidic and non-sulfidic sites. Our results indicate that P. thermalis' body shape has evolved in convergence with other sulfide spring populations in the genus. Phylogenetic analyses placed P. thermalis as most closely related to one population of P. sulphuraria, and population genetic analyses demonstrated that P. thermalis is genetically isolated from both P. mexicana ecotypes and P. sulphuraria. Based on these findings, we make taxonomic recommendations for P. thermalis. Overall, our study verifies the role of hydrogen sulfide as a main factor shaping convergent, phenotypic evolution and the emergence of reproductive isolation between Poecilia populations residing in adjacent sulfidic and non-sulfidic environments.