50년 만에 진화한 닭, 넌 누구니? Mitogenomic analysis of a 50-generation chicken pedigree reveals a rapid rate of mitochondrial evolution and evidence for paternal mtDNA inheritance

Mitogenomic analysis of a 50-generation chicken pedigree reveals a rapid rate of mitochondrial evolution and evidence for paternal mtDNA inheritance

50년 만에 진화한 닭, 넌 누구니?

英 연구진, 50년 만에 유전자 돌연변이 발생한 닭 발견

연구진이 진화의 흔적을 발견한 플리머스록 품종. 1957년부터 개량하는 과정에서 같은 품종이지만 개체 사이

에 크기가 10배 이상 차이 나기도 한다. - 미국 버지니아공대 / 존 맥코믹 제공

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생물의 진화가 기존에 알려진 것보다 훨씬 빠르게 일어난다는 연구 결과가 나왔다.   그레거 라르손 영국 옥스퍼드대 고고학과 교수팀은 ‘플리머스록’ 품종의 닭이 진화 속도가 빠르다는 사실을 발견해 ‘생물학 소식(Biology Letters)’ 28일 자 온라인판에 발표했다.    플리머스록 품종은 1957년 폴 지겔 미국 버지니아공대 농생명공학과 교수가 개량한 종이다. 크기가 큰 수탉은 큰 암탉과, 작은 수탉은 작은 암탉과 선택적으로 교배했기 때문에 같은 종이라도 개체에 따라 몸 크기가 10배 이상 차이나기도 한다. 특히 50여 년에 걸쳐 53세대에 이르는 닭의 족보가 오롯이 보존돼 있어 유전학 실험에 많이 쓰인다.   연구팀은 같은 세대의 닭 12마리에서 혈액을 채취해 유전자 돌연변이가 있는지 살펴봤다. 그 결과 미토콘드리아 유전자 중 2곳(ND4L, CYTB)에서 돌연변이가 나타난 사실을 확인했다. 50년 만에 유전자 돌연변이가 발생한 것이다.   라르손 교수는 “돌연변이는 보통 100만 년 동안에 2% 정도의 확률로 일어난다고 추정돼 왔지만 50년 만에도 돌연변이가 발생한다는 사실을 확인한 것”이라며 “이는 실제로 진화가 훨씬 빠르게 일어날 수 있음을 의미한다”고 밝혔다.     한편 연구팀은 유전자를 분석하는 과정에서 닭의 경우 미토콘드리아를 수컷에게서 받는다는 사실도 발견했다.   지금까지 꿀벌, 매미, 홍합 등 일부 동물에서만 미토콘드리아가 부계 유전되는 것으로 확인됐을 뿐 사람을 비롯한 대부분 유성생식생물은 미토콘드리아가 모계유전 되는 것으로 알려졌다.  동아사이언스 염재윤 기자 dsjy@donga.com

 

Michelle Alexander, Simon Y. W. Ho, Martyna Molak, Ross Barnett, Örjan Carlborg, Ben Dorshorst, Christa Honaker, Francois Besnier, Per Wahlberg, Keith Dobney, Paul Siegel, Leif Andersson, Greger Larson

Abstract

Mitochondrial genomes represent a valuable source of data for evolutionary research, but studies of their short-term evolution have typically been limited to invertebrates, humans and laboratory organisms. Here we present a detailed study of 12 mitochondrial genomes that span a total of 385 transmissions in a well-documented 50-generation pedigree in which two lineages of chickens were selected for low and high juvenile body weight. These data allowed us to test the hypothesis of time-dependent evolutionary rates and the assumption of strict maternal mitochondrial transmission, and to investigate the role of mitochondrial mutations in determining phenotype. The identification of a non-synonymous mutation in ND4L and a synonymous mutation in CYTB, both novel mutations in Gallus, allowed us to estimate a molecular rate of 3.13 × 10−7 mutations/site/year (95% confidence interval 3.75 × 10−8–1.12 × 10−6). This is substantially higher than avian rate estimates based upon fossil calibrations. Ascertaining which of the two novel mutations was present in an additional 49 individuals also revealed an instance of paternal inheritance of mtDNA. Lastly, an association analysis demonstrated that neither of the point mutations was strongly associated with the phenotypic differences between the two selection lines. Together, these observations reveal the highly dynamic nature of mitochondrial evolution over short time periods.

1. Introduction

Mitochondrial genomes have been widely used in biological research, especially when studying evolutionary and demographic processes that occur over short timeframes [1]. In vertebrates, mitochondrial evolution is characterized by strictly maternal inheritance and lack of recombination. Although various studies have suggested a constant rate of mitochondrial evolution among lineages and through time [2], there is now considerable evidence of a disparity between short- and long-term estimates of mitochondrial substitution rates [3–5]. Among the possible explanations for this pattern is that mitochondrial DNA (mtDNA) evolves non-neutrally, such that purifying selection removes negative mutations over time [6]. This naturally produces a pattern in which transient, deleterious mutations cause a short-term elevation in rates.

There have been few studies of short-term mitochondrial evolution, including both mutation rates and paternal leakage, particularly in non-human vertebrates [7,8]. Estimates of mitogenomic mutation rates have been obtained in studies of Adélie penguins [6,9] and humans [10] and these rates greatly exceed those inferred from longer phylogenetic timescales. Evidence for paternal inheritance of mtDNA (and other ‘rare’ evolutionary phenomena) is accumulating in multiple species, including humans [11] and sheep [12], but it is usually only visible in laboratory or controlled conditions [13–15]. As a result, its frequency may be underappreciated. This is compounded by the assumption that in natural populations, without direct knowledge of genetic relatedness and transmission, all mtDNA is maternally inherited. Combined with the low power associated with standard detection methodologies, it has been difficult to assess rates of paternal leakage in natural populations [13].

Domesticated animals present ideal systems for studying mitochondrial evolution in vertebrates, particularly if they have documented pedigrees. One such pedigree has been recorded for the Virginia chicken lines, an experimental White Plymouth Rock population spanning more than 50 generations. This pedigree, initiated in a founder population of seven partially inbred lines, was subjected to annual divergent selection for high and low body-weights at 56 days of age. This approach established high (HWS) and low (LWS) weight selected lines that now possess a greater than 10-fold difference in body weight at selection age [16–18].

Here, we used this well-documented chicken pedigree to perform a detailed investigation of short-term mitochondrial evolution in a vertebrate system. More specifically, we estimated the mitochondrial mutation rate, tested for instances of non-maternal inheritance, and examined the degree to which mitochondrial mutations were responsible for the divergent phenotypes of the two selected lines.

2. Material and methods

We identified and sequenced the mitogenomes of the 12 most distantly related individuals on the maternal pedigree, representing 385 mitochondrial transmissions. This sampling scheme provided an efficient means of capturing a large number of mitochondrial transmissions with a limited sample of mitogenomes (figure 1a). We used multiple overlapping PCR and Sanger sequencing primer pairs (electronic supplementary material, table S2) and aligned the resulting genomes using CodonCode (http://www.codoncode.com. CodonCode Corporation).

Figure 1.

Chicken pedigree from which mitochondrial genomes were sequenced. (a) Overview of the maternal lineages of the chicken pedigree, comprising high weight selected (HWS) and low weight selected (LWS) lines. Pink circles indicate individuals from which we sequenced complete mitochondrial genomes and grey circles represent those that were typed for the mutations in CYTB and ND4L. Black circles indicate individuals that were either not sampled or not successfully sampled. Codes on the left-hand side refer to generations before (P) and after (S) the selection experiment began, and following the initiation of the inter-cross experiments (F). The numerals 1 and 2 level with the chicken figures refer to the two maternal lines present in the HWS and LWS, respectively. (b) Subset of the pedigree from S13 to F8 and additional detail of the LWS line. Blue and yellow shading indicates the timing and lineage on which the ND4L and CYTB mutations occurred on the pedigree, respectively. Genotyped individuals that possessed the ND4L mutation are shown in blue and those that were heteroplasmic for ND4L are shown in white and blue. Those that possessed both mutations but were heteroplasmic for the CYTB mutation are shown in green and blue, the individual that was homoplasmic for both mutations is shown in green. Those that were tested but possessed neither mutation are shown in white. The blue arrow represents the instance of paternal leakage. It starts on the lineage from which the male involved in the paternal leakage was derived, and points to the female whose offspring inherited the male's mitochondrial genome. Further details are in the electronic supplementary material.

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http://rsbl.royalsocietypublishing.org/content/11/10/20150561

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