Whole-genome analysis reveals the diversification of Galapagos rail (Aves: Rallidae) and confirms the success of goat eradication programs.

Similar to other insular birds around the world, the Galapagos rail (Laterallus spilonota Gould, 1841) exhibits reduced flight capacity following its colonization of the archipelago ~1.2 mya. Despite their short evolutionary history, rails have colonized seven different islands spanning the entire width of the archipelago. Galapagos rails were once common on islands with sufficiently high altitudes to support shrubs in humid habitats. After humans introduced goats, this habitat was severely reduced due to overgrazing. Habitat loss devastated some rail populations, with less than 50 individuals surviving, rendering the genetic diversity of Galapagos rail a pressing conservation concern. Additionally, one enigma is the reappearance of rails on the island of Pinta after they were considered extirpated. Our approach was to investigate the evolutionary history and geographic distribution of Galapagos rails as well as examine the genome-wide effects of historical population bottlenecks using 39 whole genomes across different island populations. We recovered an early divergence of rail ancestors leading to the isolated populations on Pinta and a second clade comprising the rest of the islands, historically forming a single landmass. Subsequently, the separation of the landmass ~900 kya may have led to the isolation of the Isabela population with more panmictic populations found on Santa Cruz and Santiago islands. We found that rails genomes contain long runs of homozygosity (>2 Mb) that could be related to the introduction of goats. Finally, our findings show that the modern eradication of goats was critical to avoiding episodes of inbreeding in most populations.

The genomic footprint of whaling and isolation in fin whale populations.

Twentieth century industrial whaling pushed several species to the brink of extinction, with fin whales being the most impacted. However, a small, resident population in the Gulf of California was not targeted by whaling. Here, we analyzed 50 whole-genomes from the Eastern North Pacific (ENP) and Gulf of California (GOC) fin whale populations to investigate their demographic history and the genomic effects of natural and human-induced bottlenecks. We show that the two populations diverged ~16,000 years ago, after which the ENP population expanded and then suffered a 99% reduction in effective size during the whaling period. In contrast, the GOC population remained small and isolated, receiving less than one migrant per generation. However, this low level of migration has been crucial for maintaining its viability. Our study exposes the severity of whaling, emphasizes the importance of migration, and demonstrates the use of genome-based analyses and simulations to inform conservation strategies.

Comparative genomics uncovers the evolutionary history, demography, and molecular adaptations of South American canids.

The remarkable radiation of South American (SA) canids produced 10 extant species distributed across diverse habitats, including disparate forms such as the short-legged, hypercarnivorous bush dog and the long-legged, largely frugivorous maned wolf. Despite considerable research spanning nearly two centuries, many aspects of their evolutionary history remain unknown. Here, we analyzed 31 whole genomes encompassing all extant SA canid species to assess phylogenetic relationships, interspecific hybridization, historical demography, current genetic diversity, and the molecular bases of adaptations in the bush dog and maned wolf. We found that SA canids originated from a single ancestor that colonized South America 3.9 to 3.5 Mya, followed by diversification east of the Andes and then a single colonization event and radiation of Lycalopex species west of the Andes. We detected extensive historical gene flow between recently diverged lineages and observed distinct patterns of genomic diversity and demographic history in SA canids, likely induced by past climatic cycles compounded by human-induced population declines. Genome-wide scans of selection showed that disparate limb proportions in the bush dog and maned wolf may derive from mutations in genes regulating chondrocyte proliferation and enlargement. Further, frugivory in the maned wolf may have been enabled by variants in genes associated with energy intake from short-chain fatty acids. In contrast, unique genetic variants detected in the bush dog may underlie interdigital webbing and dental adaptations for hypercarnivory. Our analyses shed light on the evolution of a unique carnivoran radiation and how it was shaped by South American topography and climate change.

Puma genomes from North and South America provide insights into the genomic consequences of inbreeding.

Pumas are the most widely distributed felid in the Western Hemisphere. Increasingly, however, human persecution and habitat loss are isolating puma populations. To explore the genomic consequences of this isolation, we assemble a draft puma genome and a geographically broad panel of resequenced individuals. We estimate that the lineage leading to present-day North American pumas diverged from South American lineages 300-100 thousand years ago. We find signatures of close inbreeding in geographically isolated North American populations, but also that tracts of homozygosity are rarely shared among these populations, suggesting that assisted gene flow would restore local genetic diversity. The genome of a Florida panther descended from translocated Central American individuals has long tracts of homozygosity despite recent outbreeding. This suggests that while translocations may introduce diversity, sustaining diversity in small and isolated populations will require either repeated translocations or restoration of landscape connectivity. Our approach provides a framework for genome-wide analyses that can be applied to the management of similarly small and isolated populations.

Phylogeographic and diversification patterns of the white-nosed coati (Nasua narica): Evidence for south-to-north colonization of North America.

White-nosed coatis (Nasua narica) are widely distributed throughout North, Central, and South America, but the patterns of temporal and spatial diversification that have contributed to this distribution are unknown. In addition, the biogeographic history of procyonid species in the Americas remains contentious. Using sequences from three mitochondrial loci (Cytochrome b, NAHD5 and 16S rRNA; 2201 bp) and genotypes from 11 microsatellite loci, we analyzed genetic diversity to determine phylogeographic patterns, genetic structure, divergence times, and gene flow among Nasua narica populations throughout the majority of the species' range. We also estimated the ancestral geographic range of N. narica and other procyonid species. We found a high degree of genetic structure and divergence among populations that conform to five evolutionarily significant units. The most southerly distributed population (Panama) branched off much earlier (∼3.8 million years ago) than the northern populations (<1.2 million years ago). Estimated gene flow among populations was low and mostly northwards and westwards. The phylogeographic patterns within N. narica are associated with geographic barriers and habitat shifts likely caused by Pliocene-Pleistocene climate oscillations. Significantly, our findings suggest the dispersal of N. narica was south-to-north beginning in the Pliocene, not in the opposite direction during the Pleistocene as suggested by the fossil record, and that the most recent common ancestor for coati species was most likely distributed in South or Central America six million years ago. Our study implies the possibility that the diversification of Nasua species, and other extant procyonid lineages, may have occurred in South America.

Propiedades biológicas de los alérgenos inhalatorios y su relación con la respuesta inmunitaria / Biological properties of inhalant aeroallergens and their relation to immune responses

IgE-binding studies show that many of the common causes of inhalant allergy such as grass, olive, ragweed and birch pollen, house dust mites and some fungi have one or a few principal allergens that can account for most of the allergic response. The IgE binding to allergens from other sources can be more evenly spread amongst different proteins or, as indicated in cat allergy, varies with clinical presentation. The biological properties of nearly all of the principal allergens can now be predicted from the knowledge of their structures and they point to likely interactions with the innate immune system, as well as possible interactions with hormonal regulators of immunity. As found for pectate lyases and the Ole e1-like proteins, biologically similar proteins can be principal allergens for many species while the Dermatophagoides spp. and Blomia tropicalis allergens show that allergens with the same biological properties reveal interspecies variation in allergen hierarchy. These properties show that the interactions of allergens with innate immunity and immuno-regulators will be different for different allergens, and this concurs with the evidence that immune responses to allergens from the same source are regulated independently, as are responses to co-presented allergenic and non-allergenic proteins

Los estudios de unión con la IgE demostraron que muchas de las causas comunes de alergia inhalatoria, como a las gramíneas, el olivo, la ambrosía, el polen de abedul, los ácaros del polvo doméstico y algunos hongos, tienen uno o unos pocos de los alérgenos principales que pueden representar la mayoría de las respuestas alérgicas. La IgE que se une a los alérgenos de otras fuentes puede diseminarse entre diferentes proteínas o, como indica la alergia al gato, varía con la presentación clínica. Las propiedades biológicas de casi todos los alérgenos principales pueden actualmente predecirse a partir del conocimiento de sus estructuras e indican las interacciones probables con el sistema inmunitario innato, así como las interacciones posibles con los reguladores hormonales de la inmunidad. Como se encontró para las pectato liasas y las proteínas similares a Ole e1, las proteínas biológicamente similares pueden ser los alérgenos principales para muchas especies, mientras que los alérgenos Dermatophagoides spp. y Blomia tropicalis muestran que los alérgenos con las mismas propiedades biológicas tienen variación entre las especies en la jerarquía alergénica. Estas propiedades demuestran que las interacciones de los alérgenos con la inmunidad innata y los inmunorreguladores serían diferentes para los distintos alérgenos, y esto coincide con las pruebas que indican que las respuestas inmunes a los alérgenos de la misma fuente sufren una regulación por aumento (upregulation), independientemente de si son respuestas a las proteínas co-presentadas alergénicas y no alergénicas

Molecular assessment of the phylogeny and biogeography of a recently diversified endemic group of South American canids (Mammalia: Carnivora: Canidae).

To investigate the evolution and biogeography of an endemic group of South American foxes, we examined mitochondrial DNA control region sequences for 118 individuals belonging to all six extant species of the genus Lycalopex. Phylogenetic and molecular dating analyses supported the inference that this genus has undergone a very recent and rapid radiation, stemming from a common ancestor that lived ca. 1 million years ago. The Brazilian endemic L. vetulus was supported as the most basal species in this genus, whereas the most internal group is comprised by the recently diverged (ca. 350,000 years ago) Andean/Patagonian species L. griseus and L. culpaeus. We discuss the inferred phylogenetic relationships and divergence times in the context of the current geographic distributions of these species, and the likely effects of Pleistocene climatic changes on the biogeography of this group. Furthermore, a remarkable finding was the identification of multiple individuals classified as L. gymnocercus bearing mtDNA haplotypes clearly belonging to L. griseus, sampled in regions where the latter is not known to occur. At a minimum, this result implies the need to clarify the present-day geographic distribution of each of these fox species, while it may also indicate an ongoing hybridization process between them. Future testing of this hypothesis with in-depth analyses of these populations is thus a priority for understanding the history, evolutionary dynamics and present-day composition of this endemic Neotropical genus.

Intraspecific morphological and genetic variation of common species predicts ranges of threatened ones.

Predicting where threatened species occur is useful for making informed conservation decisions. However, because they are usually rare, surveying threatened species is often expensive and time intensive. Here, we show how regions where common species exhibit high genetic and morphological divergence among populations can be used to predict the occurrence of species of conservation concern. Intraspecific variation of common species of birds, bats and frogs from Ecuador were found to be a significantly better predictor for the occurrence of threatened species than suites of environmental variables or the occurrence of amphibians and birds. Fully 93 per cent of the threatened species analysed had their range adequately represented by the geographical distribution of the morphological and genetic variation found in seven common species. Both higher numbers of threatened species and greater genetic and morphological variation of common species occurred along elevation gradients. Higher levels of intraspecific divergence may be the result of disruptive selection and/or introgression along gradients. We suggest that collecting data on genetic and morphological variation in common species can be a cost effective tool for conservation planning, and that future biodiversity inventories include surveying genetic and morphological data of common species whenever feasible.

Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences.

The mammalian order Carnivora has attracted the attention of scientists of various disciplines for decades, leading to intense interest in defining its supra-familial relationships. In the last few years, major changes to the topological structure of the carnivoran tree have been proposed and supported by various molecular data sets, radically changing the traditional view of family composition in this order. Although a sequence of molecular studies have established a growing consensus with respect to most inter-familial relationships, no analysis so far has included all carnivoran lineages (both feliform and caniform) in an integrated data set, so as to determine comparative patterns of diversification. Moreover, no study conducted thus far has estimated divergence dates among all carnivoran families, which is an important requirement in the attempt to understand the patterns and tempo of diversification in this group. In this study, we have investigated the phylogenetic relationships among carnivoran families, and performed molecular dating analyses of the inferred nodes. We assembled a molecular supermatrix containing 14 genes (7765 bp), most of which have not been previously used in supra-familial carnivoran phylogenetics, for 50 different genera representing all carnivoran families. Analysis of this data set led to consistent and robust resolution of all supra-familial nodes in the carnivoran tree, and allowed the construction of a molecular timescale for the evolution of this mammalian order.

Characterization of 12 polymorphic microsatellite markers for a facultatively eusocial sweat bee (Megalopta genalis).

We developed a library of twelve polymorphic di- and tri-nucleotide microsatellite markers for Megalopta genalis, a facultatively eusocial sweat bee. We tested each locus in a panel of 23 unrelated females and found 7-20 alleles per locus. Observed and expected heterozygosities ranged from 0.65 to 0.96 and from 0.69 to 0.95 respectively. None of the loci deviated from Hardy-Weinberg equilibrium proportions or was found to be in gametic disequilibrium.

Legacy lost: genetic variability and population size of extirpated US grey wolves (Canis lupus).

By the mid 20th century, the grey wolf (Canis lupus) was exterminated from most of the conterminous United States (cUS) and Mexico. However, because wolves disperse over long distances, extant populations in Canada and Alaska might have retained a substantial proportion of the genetic diversity once found in the cUS. We analysed mitochondrial DNA sequences of 34 pre-extermination wolves and found that they had more than twice the diversity of their modern conspecifics, implying a historic population size of several hundred thousand wolves in the western cUS and Mexico. Further, two-thirds of the haplotypes found in the historic sample are unique. Sequences from Mexican grey wolves (C. l. baileyi) and some historic grey wolves defined a unique southern clade supporting a much wider geographical mandate for the reintroduction of Mexican wolves than currently planned. Our results highlight the genetic consequences of population extinction within Ice Age refugia and imply that restoration goals for grey wolves in the western cUS include far less area and target vastly lower population sizes than existed historically.

Ancient DNA evidence for Old World origin of New World dogs.

Mitochondrial DNA sequences isolated from ancient dog remains from Latin America and Alaska showed that native American dogs originated from multiple Old World lineages of dogs that accompanied late Pleistocene humans across the Bering Strait. One clade of dog sequences was unique to the New World, which is consistent with a period of geographic isolation. This unique clade was absent from a large sample of modern dogs, which implies that European colonists systematically discouraged the breeding of native American dogs.