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1.
Mol Biol Evol ; 31(8): 2004-17, 2014 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-24903145

RESUMO

Ursine bears are a mammalian subfamily that comprises six morphologically and ecologically distinct extant species. Previous phylogenetic analyses of concatenated nuclear genes could not resolve all relationships among bears, and appeared to conflict with the mitochondrial phylogeny. Evolutionary processes such as incomplete lineage sorting and introgression can cause gene tree discordance and complicate phylogenetic inferences, but are not accounted for in phylogenetic analyses of concatenated data. We generated a high-resolution data set of autosomal introns from several individuals per species and of Y-chromosomal markers. Incorporating intraspecific variability in coalescence-based phylogenetic and gene flow estimation approaches, we traced the genealogical history of individual alleles. Considerable heterogeneity among nuclear loci and discordance between nuclear and mitochondrial phylogenies were found. A species tree with divergence time estimates indicated that ursine bears diversified within less than 2 My. Consistent with a complex branching order within a clade of Asian bear species, we identified unidirectional gene flow from Asian black into sloth bears. Moreover, gene flow detected from brown into American black bears can explain the conflicting placement of the American black bear in mitochondrial and nuclear phylogenies. These results highlight that both incomplete lineage sorting and introgression are prominent evolutionary forces even on time scales up to several million years. Complex evolutionary patterns are not adequately captured by strictly bifurcating models, and can only be fully understood when analyzing multiple independently inherited loci in a coalescence framework. Phylogenetic incongruence among gene trees hence needs to be recognized as a biologically meaningful signal.


Assuntos
Fluxo Gênico , Análise de Sequência de DNA/métodos , Ursidae/genética , Cromossomo Y/genética , Animais , Núcleo Celular/genética , Evolução Molecular , Especiação Genética , Íntrons , Masculino , Mitocôndrias/genética , Filogenia , Ursidae/classificação
2.
Mol Biol Evol ; 31(6): 1353-63, 2014 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-24667925

RESUMO

Brown and polar bears have become prominent examples in phylogeography, but previous phylogeographic studies relied largely on maternally inherited mitochondrial DNA (mtDNA) or were geographically restricted. The male-specific Y chromosome, a natural counterpart to mtDNA, has remained underexplored. Although this paternally inherited chromosome is indispensable for comprehensive analyses of phylogeographic patterns, technical difficulties and low variability have hampered its application in most mammals. We developed 13 novel Y-chromosomal sequence and microsatellite markers from the polar bear genome and screened these in a broad geographic sample of 130 brown and polar bears. We also analyzed a 390-kb-long Y-chromosomal scaffold using sequencing data from published male ursine genomes. Y chromosome evidence support the emerging understanding that brown and polar bears started to diverge no later than the Middle Pleistocene. Contrary to mtDNA patterns, we found 1) brown and polar bears to be reciprocally monophyletic sister (or rather brother) lineages, without signals of introgression, 2) male-biased gene flow across continents and on phylogeographic time scales, and 3) male dispersal that links the Alaskan ABC islands population to mainland brown bears. Due to female philopatry, mtDNA provides a highly structured estimate of population differentiation, while male-biased gene flow is a homogenizing force for nuclear genetic variation. Our findings highlight the importance of analyzing both maternally and paternally inherited loci for a comprehensive view of phylogeographic history, and that mtDNA-based phylogeographic studies of many mammals should be reevaluated. Recent advances in sequencing technology render the analysis of Y-chromosomal variation feasible, even in nonmodel organisms.


Assuntos
Cromossomos de Mamíferos , DNA/análise , Fluxo Gênico , Ursidae/genética , Cromossomo Y , Animais , Evolução Molecular , Feminino , Especiação Genética , Variação Genética , Haplótipos , Masculino , Repetições de Microssatélites , Filogenia , Filogeografia , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA , Fatores Sexuais , Irmãos , Ursidae/classificação
3.
BMC Evol Biol ; 14: 219, 2014 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-25927851

RESUMO

BACKGROUND: The current taxonomy of the African giraffe (Giraffa camelopardalis) is primarily based on pelage pattern and geographic distribution, and nine subspecies are currently recognized. Although genetic studies have been conducted, their resolution is low, mainly due to limited sampling. Detailed knowledge about the genetic variation and phylogeography of the South African giraffe (G. c. giraffa) and the Angolan giraffe (G. c. angolensis) is lacking. We investigate genetic variation among giraffe matrilines by increased sampling, with a focus on giraffe key areas in southern Africa. RESULTS: The 1,562 nucleotides long mitochondrial DNA dataset (cytochrome b and partial control region) comprises 138 parsimony informative sites among 161 giraffe individuals from eight populations. We additionally included two okapis as an outgroup. The analyses of the maternally inherited sequences reveal a deep divergence between northern and southern giraffe populations in Africa, and a general pattern of distinct matrilineal clades corresponding to their geographic distribution. Divergence time estimates among giraffe populations place the deepest splits at several hundred thousand years ago. CONCLUSIONS: Our increased sampling in southern Africa suggests that the distribution ranges of the Angolan and South African giraffe need to be redefined. Knowledge about the phylogeography and genetic variation of these two maternal lineages is crucial for the development of appropriate management strategies.


Assuntos
DNA Mitocondrial/genética , Ruminantes/classificação , Ruminantes/genética , África Austral , Angola , Animais , Sequência de Bases , Citocromos b/genética , DNA Mitocondrial/análise , Feminino , Variação Genética , Humanos , Dados de Sequência Molecular , Filogenia , Filogeografia
4.
Sci Rep ; 7: 46487, 2017 04 19.
Artigo em Inglês | MEDLINE | ID: mdl-28422140

RESUMO

Bears are iconic mammals with a complex evolutionary history. Natural bear hybrids and studies of few nuclear genes indicate that gene flow among bears may be more common than expected and not limited to polar and brown bears. Here we present a genome analysis of the bear family with representatives of all living species. Phylogenomic analyses of 869 mega base pairs divided into 18,621 genome fragments yielded a well-resolved coalescent species tree despite signals for extensive gene flow across species. However, genome analyses using different statistical methods show that gene flow is not limited to closely related species pairs. Strong ancestral gene flow between the Asiatic black bear and the ancestor to polar, brown and American black bear explains uncertainties in reconstructing the bear phylogeny. Gene flow across the bear clade may be mediated by intermediate species such as the geographically wide-spread brown bears leading to large amounts of phylogenetic conflict. Genome-scale analyses lead to a more complete understanding of complex evolutionary processes. Evidence for extensive inter-specific gene flow, found also in other animal species, necessitates shifting the attention from speciation processes achieving genome-wide reproductive isolation to the selective processes that maintain species divergence in the face of gene flow.


Assuntos
Evolução Molecular , Fluxo Gênico , Genoma , Filogenia , Ursidae/genética , Animais
5.
Curr Biol ; 26(18): 2543-2549, 2016 09 26.
Artigo em Inglês | MEDLINE | ID: mdl-27618261

RESUMO

Traditionally, one giraffe species and up to eleven subspecies have been recognized [1]; however, nine subspecies are commonly accepted [2]. Even after a century of research, the distinctness of each giraffe subspecies remains unclear, and the genetic variation across their distribution range has been incompletely explored. Recent genetic studies on mtDNA have shown reciprocal monophyly of the matrilines among seven of the nine assumed subspecies [3, 4]. Moreover, until now, genetic analyses have not been applied to biparentally inherited sequence data and did not include data from all nine giraffe subspecies. We sampled natural giraffe populations from across their range in Africa, and for the first time individuals from the nominate subspecies, the Nubian giraffe, Giraffa camelopardalis camelopardalis Linnaeus 1758 [5], were included in a genetic analysis. Coalescence-based multi-locus and population genetic analyses identify at least four separate and monophyletic clades, which should be recognized as four distinct giraffe species under the genetic isolation criterion. Analyses of 190 individuals from maternal and biparental markers support these findings and further suggest subsuming Rothschild's giraffe into the Nubian giraffe, as well as Thornicroft's giraffe into the Masai giraffe [6]. A giraffe survey genome produced valuable data from microsatellites, mobile genetic elements, and accurate divergence time estimates. Our findings provide the most inclusive analysis of giraffe relationships to date and show that their genetic complexity has been underestimated, highlighting the need for greater conservation efforts for the world's tallest mammal.


Assuntos
Especiação Genética , Girafas/classificação , Girafas/genética , África , Animais , DNA Mitocondrial/genética , Variação Genética , Tipagem de Sequências Multilocus , Filogenia
6.
Genome Biol Evol ; 7(7): 2010-22, 2015 May 27.
Artigo em Inglês | MEDLINE | ID: mdl-26019166

RESUMO

The male-inherited Y chromosome is the major haploid fraction of the mammalian genome, rendering Y-linked sequences an indispensable resource for evolutionary research. However, despite recent large-scale genome sequencing approaches, only a handful of Y chromosome sequences have been characterized to date, mainly in model organisms. Using polar bear (Ursus maritimus) genomes, we compare two different in silico approaches to identify Y-linked sequences: 1) Similarity to known Y-linked genes and 2) difference in the average read depth of autosomal versus sex chromosomal scaffolds. Specifically, we mapped available genomic sequencing short reads from a male and a female polar bear against the reference genome and identify 112 Y-chromosomal scaffolds with a combined length of 1.9 Mb. We verified the in silico findings for the longer polar bear scaffolds by male-specific in vitro amplification, demonstrating the reliability of the average read depth approach. The obtained Y chromosome sequences contain protein-coding sequences, single nucleotide polymorphisms, microsatellites, and transposable elements that are useful for evolutionary studies. A high-resolution phylogeny of the polar bear patriline shows two highly divergent Y chromosome lineages, obtained from analysis of the identified Y scaffolds in 12 previously published male polar bear genomes. Moreover, we find evidence of gene conversion among ZFX and ZFY sequences in the giant panda lineage and in the ancestor of ursine and tremarctine bears. Thus, the identification of Y-linked scaffold sequences from unordered genome sequences yields valuable data to infer phylogenomic and population-genomic patterns in bears.


Assuntos
Evolução Molecular , Ursidae/genética , Cromossomo Y , Animais , Feminino , Genoma , Sequenciamento de Nucleotídeos em Larga Escala , Masculino , Filogenia , Sequências Repetitivas de Ácido Nucleico , Ursidae/classificação
7.
Mol Ecol Resour ; 13(3): 362-8, 2013 May.
Artigo em Inglês | MEDLINE | ID: mdl-23347586

RESUMO

We report a new approach for molecular sex identification of extant Ursinae and Tremarctinae bears. Two Y-specific fragments (SMCY and 318.2) and one X-specific fragment (ZFX) are amplified in a multiplex PCR, yielding a double test for male-specific amplification and an internal positive control. The primers were designed and tested to be bear-specific, thereby minimizing the risk of cross-amplification in other species including humans. The high sensitivity and small amplicon sizes (100, 124, 160 base pairs) facilitate analysis of non-invasively obtained DNA material. DNA from tissue and blood as well as from 30 non-invasively collected hair and faeces yielded clear and easily interpretable results. The fragments were detected both by standard gel electrophoresis and automated capillary electrophoresis.


Assuntos
Marcadores Genéticos/genética , Fatores de Transcrição Kruppel-Like/genética , Reação em Cadeia da Polimerase Multiplex/métodos , Análise para Determinação do Sexo/métodos , Ursidae/genética , Cromossomo Y/genética , Animais , Sequência de Bases , Primers do DNA/genética , Eletroforese Capilar , Fezes/química , Feminino , Cabelo/química , Masculino , Dados de Sequência Molecular , Sensibilidade e Especificidade , Análise de Sequência de DNA , Especificidade da Espécie
8.
PLoS One ; 7(8): e42526, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22916132

RESUMO

TNF-related apoptosis-inducing ligand (TRAIL) is a member of the tumor necrosis factor (TNF) ligand family that exerts its apoptotic activity in human cells by binding to two transmembrane receptors, TRAILR1 and TRAILR2. In cells co-expressing both receptors the particular contribution of either protein to the overall cellular response is not well defined. Here we have investigated whether differences in the signaling capacities of TRAILR1 and TRAILR2 can be attributed to certain functional molecular subdomains. We generated and characterized various chimeric receptors comprising TRAIL receptor domains fused with parts from other members of the TNF death receptor family. This allowed us to compare the contribution of particular domains of the two TRAIL receptors to the overall apoptotic response and to identify elements that regulate apoptotic signaling. Our results show that the TRAIL receptor death domains are weak apoptosis inducers compared to those of CD95/Fas, because TRAILR-derived constructs containing the CD95/Fas death domain possessed strongly enhanced apoptotic capabilities. Importantly, major differences in the signaling strengths of the two TRAIL receptors were linked to their transmembrane domains in combination with the adjacent extracellular stalk regions. This was evident from receptor chimeras comprising the extracellular part of TNFR1 and the intracellular signaling part of CD95/Fas. Both receptor chimeras showed comparable ligand binding affinities and internalization kinetics. However, the respective TRAILR2-derived molecule more efficiently induced apoptosis. It also activated caspase-8 and caspase-3 more strongly and more quickly, albeit being expressed at lower levels. These results suggest that the transmembrane domains together with their adjacent stalk regions can play a major role in control of death receptor activation thereby contributing to cell type specific differences in TRAILR1 and TRAILR2 signaling.


Assuntos
Apoptose , Receptores do Ligante Indutor de Apoptose Relacionado a TNF/fisiologia , Transdução de Sinais , Animais , Linhagem Celular Transformada , Endocitose , Ligantes , Camundongos , Ligação Proteica , Receptores do Ligante Indutor de Apoptose Relacionado a TNF/metabolismo
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