The high Andes, gene flow and a stable hybrid zone shape the genetic structure of a wide-ranging South American parrot

<p>Abstract</p> <p>Background</p> <p>While the gene flow in some organisms is strongly affected by physical barriers and geographical distance, other highly mobile species are able to overcome such constraints. In southern South America, the Andes (here up to 6,900 m) may constitute a formidable barrier to dispersal. In addition, this region was affected by cycles of intercalating arid/moist periods during the Upper/Late Pleistocene and Holocene. These factors may have been crucial in driving the phylogeographic structure of the vertebrate fauna of the region. Here we test these hypotheses in the burrowing parrot <it>Cyanoliseus patagonus </it>(Aves, Psittaciformes) across its wide distributional range in Chile and Argentina.</p> <p>Results</p> <p>Our data show a Chilean origin for this species, with a single migration event across the Andes during the Upper/Late Pleistocene, which gave rise to all extant Argentinean mitochondrial lineages. Analyses suggest a complex population structure for burrowing parrots in Argentina, which includes a hybrid zone that has remained stable for several thousand years. Within this zone, introgression by expanding haplotypes has resulted in the evolution of an intermediate phenotype. Multivariate regressions show that present day climatic variables have a strong influence on the distribution of genetic heterogeneity, accounting for almost half of the variation in the data.</p> <p>Conclusions</p> <p>Here we show how huge barriers like the Andes and the regional environmental conditions imposed constraints on the ability of a parrot species to colonise new habitats, affecting the way in which populations diverged and thus, genetic structure. When contact between divergent populations was re-established, a stable hybrid zone was formed, functioning as a channel for genetic exchange between populations.</p

Extinctions, genetic erosion and conservation options for the black rhinoceros (Diceros bicornis)

The black rhinoceros is again on the verge of extinction due to unsustainable poaching in its native range. Despite a wide historic distribution, the black rhinoceros was traditionally thought of as depauperate in genetic variation, and with very little known about its evolutionary history. This knowledge gap has hampered conservation efforts because hunting has dramatically reduced the species’ once continuous distribution, leaving five surviving gene pools of unknown genetic affinity. Here we examined the range-wide genetic structure of historic and modern populations using the largest and most geographically representative sample of black rhinoceroses ever assembled. Using both mitochondrial and nuclear datasets, we described a staggering loss of 69% of the species’ mitochondrial genetic variation, including the most ancestral lineages that are now absent from modern populations. Genetically unique populations in countries such as Nigeria, Cameroon, Chad, Eritrea, Ethiopia, Somalia, Mozambique, Malawi and Angola no longer exist. We found that the historic range of the West African subspecies (D. b. longipes), declared extinct in 2011, extends into southern Kenya, where a handful of individuals survive in the Masai Mara. We also identify conservation units that will help maintain evolutionary potential. Our results suggest a complete re-evaluation of current conservation management paradigms for the black rhinoceros

Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds

Microsatellite loci are ideal for testing hypotheses relating to genetic segregation at fine spatio-temporal scales. They are also conserved among closely related species, making them potentially useful for clarifying interspecific relationships between recently diverged taxa. However, mutations at primer binding sites may lead to increased non-amplification, or disruptions that may lead to decreased polymorphism in non-target species. Furthermore, high mutation rates and constraints on allele size may also lead, with evolutionary time, to an increase in convergently evolved allele size classes, biasing measures of interspecific genetic differentiation. Here, we used next-generation sequencing to develop microsatellite markers from a shotgun genome sequence of the sub-Antarctic seabird, the thin-billed prion (Pachyptila belcheri), that we tested for cross-species amplification in other Pachyptila and related sub-Antarctic species. We found that heterozygosity decreased and the proportion of non-amplifying loci increased with phylogenetic distance from the target species. Surprisingly, we found that species trees estimated from interspecific FST provided better approximations of mtDNA relationships among the studied species than those estimated using DC, even though FST was more affected by null alleles. We observed a significantly non-linear second order polynomial relationship between microsatellite and mtDNA distances. We propose that the loss of linearity with increasing mtDNA distance stems from an increasing proportion of homoplastic allele size classes that are identical in state, but not identical by descent. Therefore, despite high cross-species amplification success and high polymorphism among the closely related Pachyptila species, we caution against the use of microsatellites in phylogenetic inference among distantly related taxa

Identification of novel microsatellite loci in the sand martin, Riparia riparia, and cross-amplification of loci from other bird species

Artículo de publicación ISIWe isolated and characterised six novel microsatellite loci for paternity analysis in the sand martin Riparia riparia, by screening an enriched genomic library. In addition, we tested 16 already published microsatellite markers, five of which were also polymorphic in the sand martin. Only one of these 11 loci exhibited evidence of null alleles, and all were polymorphic (mean Ho = 0.68, range of number of alleles per locus = 4–24), making them suitable for individual heterozygosity quantification and paternity assessment in this species (exclusion probability of 11 unlinked loci = 0.999997).This research was funded by the Austrian Academy of Sciences and by OTKA grants (T042879, K69068) awarded to T.S. Blood samples were collected under permits issued by the Hortoba´gy National Park (22- 66/2004)

Data from: Selection from parasites favors immunogenetic diversity but not divergence among locally adapted host populations

The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulfide, and represent highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans-species evolution)

Data from: Selection from parasites favors immunogenetic diversity but not divergence among locally adapted host populations

The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulfide, and represent highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans-species evolution)

Fasta Genbank 80 MHC haplotypes

This fasta file contains the DNA sequences of the 80 unique MHC Class IIB alleles that were isolated in this study. Each of our six subpopulations have different combinations of these alleles

2 Microsatellite haplotypes

This file includes the raw microsatellite data of hosts investigated across 6 sites. Variables include an individual identification number, population of origin for each host individual, and allele lengths for 12 microsatellite loci of each individual host. Sequence data is available through Genbank

4 BSD temporal variation

Raw data of the presence of black spot disease (BSD; Uvulifer sp.) across a temporal series of samples from all 6 population investigated in this study. Variables included are year of collection, habitat type, population of origin, as well as the number of Uvulifer cysts and the presence or absence of Uvulifer cysts. Note that data is not available for all populations and all years (see main manuscript) and that only presence/absence data was available for some years

1 Parasite communities

This file includes the raw data about the occurrence of parasites across 6 sites investigated in the study. Included are data for individual hosts and counts of specific parasites as outlined in the paper. Variables include an individual identification number (which is also used for the MHC and microsatellite data), population of origin for each host individual, sex, standard length (in millimeter), as well as the number of Oodinium, Ambiphyra, Trichodina, Dactylogyrus, Gyrodactylus, Diplostomum cf. spathaceum, Echinochasmus cf. donaldsoni, Uvulifer, Trematode 1, Trematode 2, Trematode 3, Nematode, Cestode, and Lernea recorded per host