Mendelian nightmares: The germline-restricted chromosome of songbirds

Germline-restricted chromosomes (GRCs) are accessory chromosomes that occur only in germ cells. They are eliminated from somatic cells through programmed DNA elimination during embryo development. GRCs have been observed in several unrelated animal taxa and show peculiar modes of non-Mendelian inheritance and within-individual elimination. Recent cytogenetic and phylogenomic evidence suggests that a GRC is present across the species-rich songbirds, but absent in non-passerine birds, implying that over half of all 10,500 bird species have extensive germline/soma genome differences. Here, we review recent insights gained from genomic, transcriptomic, and cytogenetic approaches with regard to the genetic content, phylogenetic distribution, and inheritance of the songbird GRC. While many questions remain unsolved in terms of GRC inheritance, elimination, and function, we discuss plausible scenarios and future directions for understanding this widespread form of programmed DNA elimination

Multilocus phylogeography of two Atlantic Forest species of Pyriglena (Aves: Thamnophilidae)

Visando contribuir para a compreensão dos processos que originaram e mantiveram a biodiversidade na Mata Atlântica (MA), o presente estudo teve como objetivo inferir a história evolutiva - bem como os processos biogeográficos envolvidos - de duas espécies de aves da MA, P. atra (120 indivíduols) e P. leucoptera (434 indivíduos). Realizamos uma análise filogeográfica envolvendo marcadores com diferentes tipos de herança: materna (gene mitocondrial da subunidade II da NADH desidrogenase), biparental (três marcadores anônimos VIDY, GK439 e 55J7) e ligada ao cromossomo Z (íntron 18 da helicase com cromo-domínio de ligação ao DNA, íntron 15 da helicase Brahma dependente de ATP e íntron 1 da fosfolipase A2). Duas questões principais foram abordadas: (i) Qual hipótese de diversificação é mais congruente com os resultados do presente estudo? (ii) Os resultados baseados em marcadores com diferentes tipos de herança são congruentes? Para responder a primeira questão, algumas das previsões de cada hipótese foram testadas. Foi encontrada evidência de que as mudanças climáticas no final do Pleistoceno parecem ter sido importantes na estrutura filogeográfica de Pyriglena atra e Pyriglena leucoptera na MA. Os resultados encontrados foram congruentes com a Hipótese dos Isolados de Montanha, mas aparentemente refutam outras hipóteses, tais como: a Hipótese dos Refúgios do Pleistoceno no contexto do modelo paleoclimático proposto por Carnaval & Moritz (2008), Hipótese de estruturas fisiográficas (rios ou montanhas) como barreiras, e a Hipótese de Gradientes Ecológicos. Além disso, os rios Doce e Contas parecem ser barreiras secundárias interrompendo parcialmente o gênico. Finalmente, os marcadores revelaram diferentes níveis de estrutura geográfica e sinais nem sempre totalmente congruentes. Assim, embora os marcadores mitocondriais sejam muito informativos em reconstruções filogeográficas, é importante usar vários tipos de marcadores para recuperar de forma mais completa a história dos processos evolutivos dos organismos e os possíveis fatores que geraram essa biodiversidadeTo contribute to the understanding of the processes that originated and maintained biodiversity in the Atlantic Forest (AF), the present study aimed to infer the evolutionary history - as well as the biogeographic processes involved - of two AF bird species, P. atra (120 individuals) and P. leucoptera (434 individuals). We performed a phylogeographic analysis based on markers with different types of inheritance: maternal (mitochondrial gene of the NADH dehydrogenase subunit II), biparental (three annonymous markers: VIDY, GK439, 55J7) and Z-linked (intron 18 of the chromo-DNA-binding domain helicase, intron 15 of the ATP-dependent Brahma helicase and intron 1 of the Phospholipase A2). Two major questions were addressed: (i) Which diversification hypothesis best fits the results of the present study? (ii) Are the results based on markers with different types of inheritance congruent? In order to answer the first question, some of the predictions of each hypothesis were tested. We found evidence that climate changes in the late Pleistocene seem to have been important for shaping the phylogeographic structure of Pyriglena atra and Pyriglena leucoptera in the AF. The results are congruent with the Montane Isolation Hypothesis but apparently refute other hypotheses, such as: The Pleistocene Refuge Hypothesis in the context of the paleoclimatic model proposed by Carnaval & Moritz (2008), Hypothesis of physiographic structures (i.e. rivers or mountains) as barriers, and the Ecological Gradients Hypothesis. Additionaly, the Doce and Contas rivers seem to act as secondary barriers partially disrupting gene flow. Finally, the markers revealed varying levels of geographical structure that were not totally congruent. Thus, although mitochondrial markers are very informative for phylogeographic reconstructions, it is important to use several types of markers in order to recover the history of the evolutionary processes of organisms and the possible factors that generate this biodiversit

Vicariance, dispersal, extinction and hybridization underlie the evolutionary history of Atlantic forest fire-eye antbirds (Aves : Thamnophilidae)

In order to gain insights into the biogeographic processes underlying biotic diversification in the Atlantic Forest (AF), we used a multi-locus approach to examine the evolutionary history of the White-shouldered Fire-eye (Pyriglena leucoptera) and the Fringe-backed Fire-eye (Pyriglena atra), two parapatric sister species endemic to the AF. We sequenced one mitochondrial, three Z chromosome-linked and three anonymous markers of 556 individuals from 66 localities. We recovered four lineages throughout the AF: P. atra and three populations within P. leucoptera. All populations diverged during the late Pleistocene and presented varying levels of admixture. One Z-linked locus showed the highest level of differentiation between the two species. On the other hand, a mitochondrial haplotype was shared extensively between them. Our data supported vicariance driving speciation along with extinction and dispersal as processes underlying intraspecific diversification. Furthermore, signatures of demographic expansion in most populations and areas of genetic admixture were recovered throughout the AF, suggesting that forest fragmentation was also important in differentiation. Genetic admixture areas are located between large rivers suggesting that AF rivers may diminish gene flow. Our results indicated a complex and dynamic biogeographic history of Pyriglena in the AF, with vicariance, extinction, dispersal and secondary contact followed by introgression likely influencing the current patterns of genetic distribution