The Origin and Genetic Status of Insular Caprines in the Eastern Mediterranean: A Case Study of Free-Ranging Goats (Capra aegagrus cretica) on Crete

The history and species status of free-ranging goats inhabiting the Eastern Mediterranean islands is discussed with reference to morphometric, archaeological and genetic findings. A case study on the free-ranging goats on Crete (Capra aegagrus cretica) is presented. The phenotype of the Cretan goat resembles that of the wild bezoar goat (C. aegagrus). However, the mitochondrial DNA of cytochrome b and d-loop sequences shows affinity with domestic goats. It has been suggested that the Cretan goat represents a feral animal that was introduced onto the island during the 6th millennium b.c. as a primitive domestic, and has retained the wild morphotype but has undergone significant genetic change. An alternative explanation, and the one that is proposed here, is that the goat was introduced onto the island in wild form and released as a food source. Subsequent introgressions with domestic animals, especially ewes, have influenced its genotype. These conclusions are applicable to other free-living goats and sheep which inhabit islands in the Eastern Mediterranean.     

Genetic structure of house mouse (Mus musculus Linnaeus 1758) populations in the Atlantic archipelago of the Azores: colonization and dispersal

We analyzed the genetic structure and relationships of house mouse (Mus musculus) populations in the remote Atlantic archipelago of the Azores using nuclear sequences and microsatellites. We typed Btk and Zfy2 to confirm that the subspecies Mus musculus domesticus was the predominant genome in the archipelago. Nineteen microsatellite loci (one per autosome) were typed in a total of 380 individuals from all nine Azorean islands, the neighbouring Madeiran archipelago (Madeira and Porto Santo islands), and mainland Portugal. Levels of heterozygosity were high on the islands, arguing against population bottlenecking. The Azorean house mouse populations were differentiated from the Portuguese and Madeiran populations and no evidence of recent migration between the three was obtained. Within the Azores, the Eastern, Western, and Central island groups tended to act as separate genetic units for house mice, with some exceptions. In particular, there was evidence of recent migration events among islands of the Central island group, whose populations were relatively undifferentiated. Santa Maria had genetically distinctive mice, which may relate to its colonization history. © 2013 The Linnean Society of London     

Evidence for Introgressive Hybridization of Captive Markhor (Capra falconeri) with Domestic Goat: Cautions for Reintroduction

Markhors (Capra falconeri) are among the most endangered mammal species, and several conservation measures, including ex situ breeding, are implemented to prevent their extinction. We studied sequence diversity and differentiation of the first hypervariable segment of the mitochondrial DNA control region among C. f. heptneri and C. f. megaceros kept in four zoos in relationship to lineages of other wild and domestic goats, to assess for the first time the level of molecular distinctness and variability among those subspecies, and to check for possible introgression by related Capra taxa, such as domestic goats. Levels of differentiation between some Capra falconeri lineages and modern domestic goats were similar to levels between other wild goat species (i.e., Capra aegagrus, Capra ibex) and domestic goats. Among pure markhor lineages, paraphyly was observed for C. f. heptneri, suggesting occurrence of shared ancestral polymorphism among markhor subspecies and/or ancient or recent gene exchange between subspecies. Interestingly, 35.7% of all studied markhors from three zoos are introgressed by the domestic goat. Furthermore, despite relatively small breeding group sizes, markhors have maintained a relatively high proportion of mtDNA variation within zoo groups. In any case, the existence of markhors introgressed with domestic goat DNA in zoos should be considered when selecting markhors for ex situ breeding programs with the aim of building up a stock for later reintroduction into the wild.     

Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication

Background

Domestic goats (Capra hircus) have been selected to play an essential role in agricultural production systems, since being domesticated from their wild progenitor, bezoar (Capra aegagrus). A detailed understanding of the genetic consequences imparted by the domestication process remains a key goal of evolutionary genomics.

Results

We constructed the reference genome of bezoar and sequenced representative breeds of domestic goats to search for genomic changes that likely have accompanied goat domestication and breed formation. Thirteen copy number variation genes associated with coat color were identified in domestic goats, among which ASIP gene duplication contributes to the generation of light coat-color phenotype in domestic goats. Analysis of rapidly evolving genes identified genic changes underlying behavior-related traits, immune response and production-related traits.

Conclusion

Based on the comparison studies of copy number variation genes and rapidly evolving genes between wild and domestic goat, our findings and methodology shed light on the genetic mechanism of animal domestication and will facilitate future goat breeding.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1606-1) contains supplementary material, which is available to authorized users.     

A dig into the past mitochondrial diversity of Corsican goats reveals the influence of secular herding practices

The goat (Capra hircus) is one of the earliest domesticated species ca. 10,500 years ago in the Middle-East where its wild ancestor, the bezoar (Capra aegagrus), still occurs. During the Neolithic dispersal, the domestic goat was then introduced in Europe, including the main Mediterranean islands. Islands are interesting models as they maintain traces of ancient colonization, historical exchanges or of peculiar systems of husbandry. Here, we compare the mitochondrial genetic diversity of both medieval and extant goats in the Island of Corsica that presents an original and ancient model of breeding with free-ranging animals. We amplified a fragment of the Control Region for 21 medieval and 28 current goats. Most of them belonged to the A haplogroup, the most worldwide spread and frequent today, but the C haplogroup is also detected at low frequency in the current population. Present Corsican goats appeared more similar to medieval goats than to other European goat populations. Moreover, 16 out of the 26 haplotypes observed were endemic to Corsica and the inferred demographic history suggests that the population has remained constant since the Middle Ages. Implications of these results on management and conservation of endangered Corsican goats currently decimated by a disease are addressed.     

Mitochondrial DNA Reveal that Domestic Goat (Capra hircus) are Genetically Affected by Two Subspecies of Bezoar (Capra aegagurus)

This article describes the complete sequences of the mitochondrial DNA displacement loop (D-loop) region and cytochrome b gene from domestic goats in Laos (Laos native) and wild goat markhor (C. falconeri). The wild goat bezoar (Capra aegagrus) has been considered to be the strongest candidate for the ancestor of the domestic goats (C. hircus); however, there is not sufficient molecular data to verify the hypothesis at present. In phylogenetic analyses, two wild goats, the markhor and the ibex (C. ibex), appeared as an outgroup, while the bezoar was located in a cluster of domestic goats. Mitochondrial haplotypes of Laos natives revealed two distinct major clusters: one was the same as the bezoar, the second, unique to Laos natives. The topology and calibrated levels of sequence divergence suggests that these clusters might represent at least two different subspecies of ancestral bezoars.     

Complex population genetic structure in the endemic Canary Island pine revealed using chloroplast microsatellite markers

The Canary archipelago, located on the northwestern Atlantic coast of Africa, is comprised of seven islands aligned from east to west, plus seven minor islets. All the islands were formed by volcanic eruptions and their geological history is well documented providing a historical framework to study colonization events. The Canary Island pine (Pinus canariensis C. Sm.), nowadays restricted to the westernmost Canary Islands (Gran Canaria, Tenerife, La Gomera, La Palma and El Hierro), is considered an old (Lower Cretaceous) relic from an ancient Mediterranean evolutionary centre. Twenty seven chloroplast haplotypes were found in Canary Island pine but only one of them was common to all populations. The distribution of haplotypic variation in P. canariensis suggested the colonization of western Canary Islands from a single continental source located close to the Mediterranean Basin. Present-day populations of Canary Island pine retain levels of genetic diversity equivalent to those found in Mediterranean continental pine species, Pinus pinaster and Pinus halepensis. A hierarchical analysis of variance (AMOVA) showed high differentiation among populations within islands (approximately 19%) but no differentiation among islands. Simple differentiation models such as isolation by distance or stepping-stone colonization from older to younger islands were rejected based on product-moment correlations between pairwise genetic distances and both geographic distances and population-age divergences. However, the distribution of cpSSR diversity within the islands of Tenerife and Gran Canaria pointed towards the importance of the role played by regional Pliocene and Quaternary volcanic activity and long-distance gene flow in shaping the population genetic structure of the Canary Island pine. Therefore, conservation strategies at the population level are strongly recommended for this species.Communicated by D.B. NealeA. Gómez and S.C. González-Martínez as joint authors     

Investigation of the genetic diversity of domestic Capra hircus breeds reared within an early goat domestication area in Iran

Background

Iran is an area of particular interest for investigating goat diversity. Archaeological remains indicate early goat domestication (about 10 000 years ago) in the Iranian Zagros Mountains as well as in the high Euphrates valley and southeastern Anatolia. In addition, mitochondrial DNA data of domestic goats and wild ancestors (C. aegagrusor bezoar) suggest a pre-domestication management of wild populations in southern Zagros and central Iranian Plateau. In this study genetic diversity was assessed in seven Iranian native goat breeds, namely Markhoz, Najdi, Taleshi, Khalkhali, Naini, native Abadeh and Turki-Ghashghaei. A total of 317 animals were characterized using 14 microsatellite loci. Two Pakistani goat populations, Pahari and Teddy, were genotyped for comparison.

Results

Iranian goats possess a remarkable genetic diversity (average expected heterozygosity of 0.671 across loci, 10.7 alleles per locus) mainly accounted for by the within-breed component (G_ST = 5.9%). Positive and highly significant F_IS values in the Naini, Turki-Ghashghaei, Abadeh and Markhoz breeds indicate some level of inbreeding in these populations. Multivariate analyses cluster Iranian goats into northern, central and western groups, with the western breeds relatively distinct from the others. Pakistani breeds show some relationship with Iranian populations, even if their position is not consistent across analyses. Gene flow was higher within regions (west, north, central) compared to between regions but particularly low between the western and the other two regions, probably due to the isolating topography of the Zagros mountain range. The Turki-Ghashghaei, Najdi and Abadeh breeds are reared in geographic areas where mtDNA provided evidence of early domestication. These breeds are highly variable, located on basal short branches in the neighbor-joining tree, close to the origin of the principal component analysis plot and, although highly admixed, they are quite distinct from those reared on the western side of the Zagros mountain range.

Conclusions

These observations call for further investigation of the nuclear DNA diversity of these breeds within a much wider geographic context to confirm or re-discuss the current hypothesis (based on maternal lineage data) of an almost exclusive contribution of the eastern Anatolian bezoar to the domestic goat gene pool.     

The Mediterranean monk seal Monachus monachus: status,biology, threats,and conservation priorities

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Natural or Naturalized? Phylogeography Suggests That the Abundant Sea Urchin Arbacia lixula Is a Recent Colonizer of the Mediterranean

We present the global phylogeography of the black sea urchin Arbacia lixula, an amphi-Atlantic echinoid with potential to strongly impact shallow rocky ecosystems. Sequences of the mitochondrial cytochrome c oxidase gene of 604 specimens from 24 localities were obtained, covering most of the distribution area of the species, including the Mediterranean and both shores of the Atlantic. Genetic diversity measures, phylogeographic patterns, demographic parameters and population differentiation were analysed. We found high haplotype diversity but relatively low nucleotide diversity, with 176 haplotypes grouped within three haplogroups: one is shared between Eastern Atlantic (including Mediterranean) and Brazilian populations, the second is found in Eastern Atlantic and the Mediterranean and the third is exclusively from Brazil. Significant genetic differentiation was found between Brazilian, Eastern Atlantic and Mediterranean regions, but no differentiation was found among Mediterranean sub-basins or among Eastern Atlantic sub-regions. The star-shaped topology of the haplotype network and the unimodal mismatch distributions of Mediterranean and Eastern Atlantic samples suggest that these populations have suffered very recent demographic expansions. These expansions could be dated 94–205 kya in the Mediterranean, and 31–67 kya in the Eastern Atlantic. In contrast, Brazilian populations did not show any signature of population expansion. Our results indicate that all populations of A. lixula constitute a single species. The Brazilian populations probably diverged from an Eastern Atlantic stock. The present-day genetic structure of the species in Eastern Atlantic and the Mediterranean is shaped by very recent demographic processes. Our results support the view (backed by the lack of fossil record) that A. lixula is a recent thermophilous colonizer which spread throughout the Mediterranean during a warm period of the Pleistocene, probably during the last interglacial. Implications for the possible future impact of A. lixula on shallow Mediterranean ecosystems in the context of global warming trends must be considered.     

A review of mammal eradications on Mediterranean islands

1. Impacts of alien invasive species on island communities and ecosystems may be even more detrimental than on the mainland. Therefore, since the 1950s, hundreds of restoration projects have been implemented worldwide, with the aim of controlling or eradicating alien species from islands. To date, no review has been focused on eradication on Mediterranean islands. To fill the gap, I reviewed the available information concerning mammal eradications so far carried out on Mediterranean islands, examining the details of several aspects of project implementation and monitoring.
2. I obtained data for 139 attempted eradications on 107 Mediterranean islands in eight countries, with Greece, Italy, and Spain accounting for the highest number. Eradication projects targeted 13 mammal species. The black rat Rattus rattus was the target of over 75% of the known attempted eradications in the Mediterranean Basin; other species targeted were feral goat Capra hircus, house mouse Mus musculus, European rabbit Oryctolagus cuniculus, and domestic cat Felis catus. The most widely adopted technique was poisoning (77% of all eradications), followed by trapping (15%) and hunting (4%). However, techniques were largely target-specific.
3. The average failure rate was about 11%. However, this percentage varied according to the specific mammalian order, and eradications of Carnivora failed more often than those of other mammals. Among rodents, house mouse eradication attained a very high failure rate (75%). Reinvasion occurred after 15% of successful eradications.
4. A better understanding of the motivations of animal rights activists may improve the chance of success when eradicating charismatic or domesticated species. Furthermore, it is crucial to collect data and case studies about reinvasions, in order to strengthen biosecurity programmes following eradication. As in other parts of the world, the next frontier in alien mammal management on Mediterranean islands concerns the eradication of invasive species from inhabited islands.

     

Life history and genetic characterisation of sea trout Salmo trutta in the Adriatic Sea

1. The brown trout Salmo trutta is characterised by both anadromous (sea trout) and resident populations, naturally occurring in Atlantic and Ponto-Caspian rivers. Sea trout are currently considered absent from rivers of the Mediterranean area, probably because of the non-optimal chemical–physical characteristics of the Mediterranean Sea. However, the occasional bycatch of smoltified S. trutta in the Adriatic Sea is well known among fishermen and the biological explanation of this phenomenon is still controversial. The aim of this study was to compare the genetic diversity of freshwater and marine brown trout to try to understand the factors underlying the presence of putative anadromous brown trout in the Adriatic Sea.
2. In this study, we analysed the genetic diversity of: (1) wild brown trout collected from the Esino River (central Italy); (2) a domestic strain of brown trout used for stocking the study area; and (3) a sample of Adriatic sea trout collected near the outlet of the Esino River. Together with genetic analysis, we carried out scale analysis in order to track the freshwater/marine stages of the life cycle in the sea trout samples. The genetic characterisation was carried out by polymerase chain reaction–restriction fragment length polymorphism analysis of the mtDNA fragment ND-5/6 and the nuclear locus LDH-C1* and by genotyping 15 microsatellite loci. The genetic polymorphism obtained was used to investigate intra- and inter-population genetic diversity, rates of genetic introgression between wild and domestic samples and the origin of sea trout specimens by using assignment tests.
3. Our genetic analyses demonstrated that the sea trout analysed in this study are from the domestic strain of Atlantic origin used in central Italy for stocking activities. The level of genetic introgression between native and domestic samples is high in the Esino River. The populations more resilient to introgressive hybridisation appeared to be those living in the portion of the river network dominated by carbonate rocks. Assignment tests (GeneClass) suggest the existence of a link between stocking efforts and the freshwater origin of the sea trout. In addition, data obtained from the analysis of scales, size measurement, and sex determination showed a pattern of smolt age, size, and sex ratio very similar to those observed in other anadromous populations.
4. In conclusion, the present study highlighted that sea trout from the central Adriatic Sea originated from brown trout of Atlantic origin inhabiting the Esino River. Their seaward migratory behaviour could represent a consequence of an active migration instead of a passive displacement by water flow. Our results also showed that traditional stocking practices represent a negative activity for the conservation of the last Mediterranean native S. trutta populations.

     

Developmental and phenotypic responses to photoperiod in uni-and bivoltine Pieris napi in California

• 1 Coastal Californian Pieris napi are facultatively bivoltine, with two seasonal phenotypes, whereas inland populations from the Inner Coast Ranges and Sierra Nevada are univoltine and monophenic.
• 2 When reared under continuous light at 25d̀C both coastal and inland stocks produce about 50% diapause pupae, which give rise to vernal-phenotype adults. Non-diapause pupae of all stocks give rise to summer-phenotype adults, even though this phenotype does not exist in the wild in univoltine populations.
• 3 Univoltinism, which implies developmental suppression of the summer phenotype, is interpreted as a derivative from multivoltinism and an adaptation to host plant phenology.

     

Habitat associations of wild goat in central Iran: implications for conservation

Wild goat (Capra aegagrus) is one of the highly valued but threatened ungulates of Iran. Seasonal habitat use of wild goat was studied from October 2006 to September 2008 in Haftad Gholleh Protected Area, central Iran. We developed averaged logistic regression models based on Akaike Information Criterion weights for each season. The obtained habitat suitability models showed high sensitivity (greater than 88%) for all evaluation datasets. Wild goat habitat use was positively related with steep slopes, areas near rocky substrates and water sources, west-facing slopes and areas far from roads in all seasons. Core zones of protected area covered nearly 70% of suitable habitats for wild goats, predicted by logistic regression models. Northern core zone covered more than 61% of predicted suitable habitats, which should receive more attention in management actions. The southern core zone boundaries should be considered to increase the encompassed suitable habitats. There was a substantial overlap between seasonal suitable habitats with the highest overlap observed between spring and summer and summer and fall.     

Contradiction in Conservation of Island Ecosystems: Plants, Introduced Herbivores and Avian Scavengers in the Canary Islands

Introduction of alien herbivores in sensitive island systems has resulted in massive effects on vegetation cover, floristic richness and composition of communities; some species can be even totally extirpated by grazing pressure. Goats Capra hircus and wild rabbits Oryctolagus cuniculus were introduced in the Canary Islands around 500 B.C. Barbary ground squirrels Atlantoxerus getulus were introduced in 1967. Traditional extensive livestock exploitations have been maintained to the present but in the last decades the number of goats has sharply increased up to densities of 53 heads/km². Overgrazing and trampling have heavily affected eleven island endemic plant species. Some populations have been reduced to less than 10 viable individuals. On the other hand, goat carcasses and wild rabbit and squirrel populations help to maintain populations of three endangered endemic subspecies of birds. This conflict presents important economic and social ramifications: whereas public funds (mainly through European LIFE projects) are devoted to conservation of plant and avian endemic taxa, the number of goats increases rapidly thanks to subventions derived from the European Common Agricultural Policy (CAP). Similar conflicts are apparent in other Mediterranean Basin insular systems. It is urgently necessary to harmonize farming and conservation objectives in the Canary Islands. The impact of goats on the vegetation should be minimized through limitation of grazing in sensitive areas with high degree of endemism. Creation of ‘vulture restaurants’ may reduce the dependence of scavengers on extensive livestock exploitations. We recommend a careful study of ecological relationships within island communities where non-native species are susceptible of playing a keystonrole as occurs in the Mediterranean Basin archipelagos.     

Phylogeographical structure in the coastal species Senecio rodriguezii (Asteraceae), a narrowly distributed endemic Mediterranean plant

Aim Our goals were (1) to assess the levels of chloroplast DNA variation in a narrowly distributed plant restricted to continental islands, (2) to ascertain whether a phylogeographical structure is present in plants restricted to coastal linear systems, and (3) to interpret the results in the light of the known palaeogeography of these islands. Location The Eastern Balearic Islands (Majorca and Minorca) in the Western Mediterranean Basin. Methods Sampling included 134 individuals from 28 populations of Senecio rodriguezii covering the entire range of the species. Sequences of the chloroplast genome (trnT–trnL spacer) were obtained and parameters of population genetic diversity and substructure were determined (h_sh_t, G_st). The geographical structure of genetic variation was assessed by an analysis of molecular variance (AMOVA). Additionally, a spatial AMOVA (SAMOVA) was used to identify groups of populations that were geographically homogeneous and maximally differentiated from each other. Finally, a pattern of isolation by distance was assessed by testing the correlation between the matrix of pairwise Φ_ST values and the matrix of geographical distances between pairs of populations using a Mantel test. Results Seven haplotypes were detected in S. rodriguezii. Only two of them were shared between islands; all of the others were restricted to Majorca (two) or Minorca (three). Overall, we found high levels of genetic diversity and significant geographical structuring of cpDNA markers. Most of the variation detected can be attributed to differences among populations (84.6%), but there was also a significant differentiation between the islands. Main conclusions Our results support the view that the Balearic Islands constitute a reservoir of genetic diversity, not only for widespread Mediterranean taxa, but also for endemic ones. The intraspecific genetic structure found in S. rodriguezii suggests that its population history was dominated by both expansion and contraction events. This has resulted in a species that is highly structured genetically, showing very few shared haplotypes between islands, and a high number of haplotypes restricted to small geographical areas within the islands. Changes in habitat availability and dynamic processes of population fragmentation and connectivity due to repeated cycles of sea‐level changes during the Quaternary are the possible underlying factors that have shaped the cpDNA pool of this endemic species on a regional scale.     

Melanocytes Fail to Survive in Hair Bulbs of the Shiba Goat (Capra hircus) With the Dominant Black-Eyed White Phenotype

Dominant black-eyed white phenotypes are one of the most commonly observed traits in domestic animals. Their genetic control mechanisms, however, have not been elucidated. As the first step to approach the problem, we examined histologically the patterns of the distribution of pigment cells in Shiba goats (two each of day-73-postcoitum and day-112-postcoitum fetuses, and a 15-week-old kid) with the dominant black-eyed white phenotype. Melanocytes were present and fully pigmented in the choroid and the sclera of eyes, as well as in dorsal skin epidermis of the fetuses and of the kid. Melanocytes were also found in approximately 6% of the hair bulbs in the fetal dorsal skin, while the rest (94%) lacked them. Hair follicles of the kid did not harbor melanocytes except for some in the early anagen stage. The results suggest that the survival of melanocytes was inhibited specifically in the hair follicles of the Shiba goat with the dominant black-eyed white phenotype and that the ostensibly similar phenotypes in the Shiba goat and in the SI or W mutants of the mouse, where melanocytes die en route to the hair bulbs, are regulated by different mechanisms.     

Long-term effects of feral goats (<Emphasis Type="Italic">Capra hircus</Emphasis>) on Mediterranean island communities: results from whole island manipulations

Islands exhibit disproportionally high biodiversity, however high levels of endemism and simplified food webs make their communities susceptible to invasive species. Introduced goats (Capra hircus), a generalist herbivore, are among the most harmful invasive species on islands. Concern about goat impacts on island communities have resulted in eradication programs, which have been generally implemented without comprehensive evaluation and monitoring. Unintended consequences may follow eradication, as grazing can have complex effects on island food webs. Using whole island manipulations, we evaluate the long-term, community-wide effects of goat herbivory, as well as their subsequent removal, in a system of 16 islands in the Aegean Sea (Greece) located within the Mediterranean biodiversity hotspot. Goat grazing on these islands is a major conservation concern, as these support endemic plant communities that have evolved in low herbivory conditions and lack appropriate defenses. We show that goat introductions lead to significant decreases in vegetation height, percent cover, and biomass but not to immediate plant species loss, as native island endemics are replaced with widespread generalist taxa carried in by the livestock. Additionally, goats contribute to the desertification of islands by initiating a long-term soil loss cycle that continues even after goats are removed; however, remaining soil structure and chemistry are not affected. Island arthropod populations do not appear to be significantly impacted by goat introduction or removal, except for a distinct increase in the order Diptera with goat presence. This study also reaffirms the role of seabirds in providing important marine subsidies, rich in nitrogen and phosphorus, to island food webs. Plant species diversity declines following goat removal, and vegetation cover returns only partially, as further recovery is being prevented by the long-term loss of soil. This suggests that following goat removal, island communities may require additional restoration efforts, including seabird reestablishment and reintroduction of extirpated plant populations, to promote island recovery.     

Evidence of potential hybridization in the Thaumetopoea pityocampa‐wilkinsoni complex

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