Evolutionary processes in an environmental challenging site: the soda-lake Natron (Tanzania).

Lakes Natron and Magadi are neighbouring small soda localised in the Eastern Rift Valley, between Kenya and Tanzania, and are the remnants of the Paleolake Orolonga after a split that occurred around 9,000 years BP. These basins represent a really harsh environment, characterized by a complex geo-morphological structure, which may increase, by habitat fragmentation and isolation, the effects of evolutionary forces (like genetic drift and selection) on the native species and populations. These lakes harbour a small species flock of quite recent origin, the Alcolapia flock, endemic of this region and not found in any other place around the world. This flock is characterized by four different morphotypes: A. alcalicus, A. latilabris, A. ndalalani, endemic of Lake Natron, and A. grahami, found only in the Lake Magadi. With the aim to understand the evolutionary processes that are shaping genetic diversity of this species, we have analysed by means of molecular genetics tools (mtDNA and nuclear DNA markers), 310 specimens of Alcolapia collected from eight populations placed around the Lake Natron and from one population located in the north-east part of Lake Magadi. Phylogenetic analyses based on D-loop sequences of a subset of 69 Alcolapia have shown a monophyletic structure of the flock, as suggested by the more frequent haplotype (2lat) shared by all the morphotypes and corresponding to the Orolonga haplotype identified in previous studies (Seegers et al, 1999; Wilson et al., 2000 and 2004). Besides, the main starburst radiation occurred in Lake Natron Alcolapia, which evolved in relatively recent times

Evolutionary processes in an environmental challenging site: the soda-lake Natron (Tanzania).

Lakes Natron and Magadi are neighbouring small soda localised in the Eastern Rift Valley, between Kenya and Tanzania, and are the remnants of the Paleolake Orolonga after a split that occurred around 9,000 years BP. These basins represent a really harsh environment, characterized by a complex geo-morphological structure, which may increase, by habitat fragmentation and isolation, the effects of evolutionary forces (like genetic drift and selection) on the native species and populations. These lakes harbour a small species flock of quite recent origin, the Alcolapia flock, endemic of this region and not found in any other place around the world. This flock is characterized by four different morphotypes: A. alcalicus, A. latilabris, A. ndalalani, endemic of Lake Natron, and A. grahami, found only in the Lake Magadi. With the aim to understand the evolutionary processes that are shaping genetic diversity of this species, we have analysed by means of molecular genetics tools (mtDNA and nuclear DNA markers), 310 specimens of Alcolapia collected from eight populations placed around the Lake Natron and from one population located in the north-east part of Lake Magadi. Phylogenetic analyses based on D-loop sequences of a subset of 69 Alcolapia have shown a monophyletic structure of the flock, as suggested by the more frequent haplotype (2lat) shared by all the morphotypes and corresponding to the Orolonga haplotype identified in previous studies (Seegers et al, 1999; Wilson et al., 2000 and 2004). Besides, the main starburst radiation occurred in Lake Natron Alcolapia, which evolved in relatively recent times

From Caves to the Savannah, the Mitogenome History of Modern Lions (Panthera leo) and Their Ancestors

Lions (Panthera leo) play a crucial ecological role in shaping and maintaining fragile ecosystems within Africa. Conservation efforts should focus on genetic variability within wild populations when considering reintroduction attempts. We studied two groups of lions from two conservation sites located in Zambia and Zimbabwe to determine their genetic make-up, information that is usually unknown to the sites. In this study, we analysed 17 specimens for cytb and seven microsatellite markers to ascertain family relationships and genetic diversity previously obtained by observational studies. We then produced a standardised haplogroup phylogeny using all available entire mitogenomes, as well as calculating a revised molecular clock. The modern lion lineage diverged ~151 kya and was divided into two subspecies, both containing three distinct haplogroups. We confirm that Panthera leo persica is not a subspecies, but rather a haplogroup of the northern P.l. leo that exited Africa at least ~31 kya. The progenitor to all lions existed ~1.2 Mya, possibly in SE Africa, and later exited Africa and split into the two cave lion lineages ~175 kya. Species demography is correlated to major climactic events. We now have a detailed phylogeny of lion evolution and an idea of their conservation status given the threat of climate change

A rapid and reliable detection procedure of Atlantic trout introgression at the diagnostic lactate dehydrogenase chain-1 gene

The Italian-native Mediterranean brown trout (Salmo ghigii) is a seriously threatened freshwater fish, especially by anthropogenic hybridisation with the domestic strains of Atlantic origin that have been repeatedly released into the wild for angling. A PCR-restriction fragment length polymorphism (RFLP) assay of the diagnostic lactate dehydrogenase chain-1 (LDH-C1) gene sequences has been routinely applied to distinguish exotic from native brown trout lineages and detect Atlantic introgression signals in the Mediterranean wild populations. Here, we used dermal swab DNA obtained from 28 wild trout to improve laboratory procedures to genetically characterise trout samples at the LDH-C1gene through (1) a capillary electrophoresis analysis of the RFLP fragments and (2) the optimisation of a diagnostic single nucleotide polymorphism analysable through mini-sequencing approaches. The developed methods were fully consistent with those obtained through the traditional approach, but their analytical process is almost entirely automated and digitalised, thus improving result readability and accuracy in the detection of alien introgressed traces in wild Mediterranean brown trout populations

Phylogeny of European Anodontini (Bivalvia: Unionidae) with a redescription of Anodonta exulcerata

Freshwater bivalves are highly threatened and globally declining due to multiple anthropogenic impacts, making them important conservation targets. Because conservation policies and actions generally occur at the species level, accurate species identification and delimitation is critical. A recent phylogenetic study of Italian mussel populations revalidated an Anodonta species bringing the number of known European Anodontini from three to four species. The current study contributes to the clarification of the taxonomy and systematics of European Anodontini, using a combination of molecular, morphological and anatomical data, and constructs phylogenies based on complete mitogenomes. A redescription of A. exulcerata and a comparative analysis of morphological and anatomical characters with respect to the other two species of Anodonta present in the area are provided. No reliable diagnostic character has emerged from comparative analysis of the morphometric characters of 109 specimens from 16 sites across the Italian peninsula. In fact, the discriminant analysis resulted in a greater probability of correct assignment to the site of origin than to the species. This confirms the difficulties of an uncritical application of visual characters for the delimitation of species, especially for Anodontinae.This research was developed under ConBiomics: the missing approach for the conservation of freshwater bivalves project Nº NORTE-01-0145-FEDER-030286, cofinanced by COMPETE 2020, Portugal 2020 and the European Union through the ERDF - European Regional Development Fund and by FCT - Fundação para a Ciência e a Tecnologia, through national funds (UID/Multi/04423/2019). FCT also supported Manuel Lopes-Lima (SFRH/BD/115728/2016).info:eu-repo/semantics/publishedVersio

Evolutionary processes in an environmental challenging site: the soda-lake Natron (Tanzania).

Lakes Natron and Magadi are neighbouring small soda localised in the Eastern Rift Valley, between Kenya and Tanzania, and are the remnants of the Paleolake Orolonga after a split that occurred around 9,000 years BP. These basins represent a really harsh environment, characterized by a complex geo-morphological structure, which may increase, by habitat fragmentation and isolation, the effects of evolutionary forces (like genetic drift and selection) on the native species and populations. These lakes harbour a small species flock of quite recent origin, the Alcolapia flock, endemic of this region and not found in any other place around the world. This flock is characterized by four different morphotypes: A. alcalicus, A. latilabris, A. ndalalani, endemic of Lake Natron, and A. grahami, found only in the Lake Magadi. With the aim to understand the evolutionary processes that are shaping genetic diversity of this species, we have analysed by means of molecular genetics tools (mtDNA and nuclear DNA markers), 310 specimens of Alcolapia collected from eight populations placed around the Lake Natron and from one population located in the north-east part of Lake Magadi. Phylogenetic analyses based on D-loop sequences of a subset of 69 Alcolapia have shown a monophyletic structure of the flock, as suggested by the more frequent haplotype (2lat) shared by all the morphotypes and corresponding to the Orolonga haplotype identified in previous studies (Seegers et al, 1999; Wilson et al., 2000 and 2004). Besides, the main starburst radiation occurred in Lake Natron Alcolapia, which evolved in relatively recent times

Past and Present Environmental Factors Differentially Influence Genetic and Morphological Traits of Italian Barbels (Pisces: <i>Cyprinidae</i>)

Local adaptation and phenotypic plasticity can lead to environment-related morphological and genetic variations in freshwater fish. Studying the responses of fish to environmental changes is crucial to understand their vulnerability to human-induced changes. Here, we used a latitudinal gradient as a proxy for past and present environmental factors and tested its influences on both genetic and morphological patterns. We selected as a suitable biogeographic model, the barbels, which inhabit 17 Adriatic basins of the central-southern Italian Peninsula, and explored association among attributes from genetic, morphological, and environmental analyses. The analysis of the mitochondrial DNA control region evidenced a southward significant increase in the number of private haplotypes, supporting the isolation of the southernmost populations related to the Mio-Pleistocene events. In contrast, morphology was mainly affected by changes in the present environmental conditions. Particularly, the number of scales and fish coloration were clearly associated to latitude, and thus thermal and hydrological conditions. Other morphometric and functional traits varied under the selective pressure of other environmental factors like elevation and distance from headwater. These results highlight the sensitivity of barbels to climate changes, which can serve as a basis for future eco-evolutionary and conservation studies

Lesser Flamingo Phoeniconaias minor as a nomadic species in African shallow alkaline lakes and pans: genetic structure and future perspectives

The Lesser Flamingo Phoeniconaias minor is a nomadic species, which inhabits shallow alkaline lakes and pans in sub-Saharan Africa and southern Asia. The extent of genetic diversity and the degree of differentiation within and among populations are important factors to determine in order to help manage and conserve the species, categorised as Near Threatened by the IUCN. This study provides an assessment of the population structure of the two largest African populations of P. minor  by genotyping six microsatellite loci from 30 individuals sampled on Lake Bogoria (Kenya) and 11 individuals from Makgadikgadi Sua Pan (Botswana). The alleles detected per locus ranged from four to 13. The Lake Bogoria population harboured 15 specific alleles, whereas the Makgadikgadi Sua Pan population only six alleles. Moderate genetic diversity (He = 0.64–0.69) was comparable with populations that have not suffered from demographic bottlenecks or inbreeding. The populations are genetically similar with little differentiation (FST and RST not significantly different from zero). Small but continuous gene flow (the estimated average number of individuals exchanged is 3–4 per generation) was found, probably reflecting the bird’s nomadic behaviour and the natural presence of temporary shallow waters between the two sampled populations. The results suggest that inbreeding effects at present are unlikely, and hence that the loss and/or degradation of its specialised habitat remains the primary concern for the species’ continued survival.OSTRICH 2011, 82(2): 95–10

Genetic Variability and Admixture Zones in the Italian Populations of Turkey Oak (<i>Quercus cerris</i> L.)

The Turkey oak (Quercus cerris L.) is widely distributed in Italy, where it is the ecologically dominant oak on sandy and acidic soil. In this work, we analysed 23 natural populations by means of eight SSR (microsatellite) markers, to obtain the first synthetic map of genetic variability for this species and to study its dispersion during the Holocene, due to the possibility that at least one refugium during the Last Glacial Maximum was in Italy. The analyses showed a good amount of genetic variability together with fair differentiation between populations, as indicated by FST = 0.059. A Bayesian analysis of the amount of admixture among populations revealed the presence of four putative gene pools of origin and a rough subdivision of the populations according to their geographic location, as confirmed by the spatial analysis. No evidence for the existence of putative refugial populations was found; however, this study paves the way for the planning of conservation strategies also with regard to the relationship between Turkey oak and other oak species in Italy