Genome-Wide Evolutionary Analysis of Natural History and Adaptation in the World’s Tigers

Liu, Yue-Chen; Sun, Xin; Driscoll, Carlos A.; Miquelle, Dale G.; Xu, Xiao; Martelli, Paolo; Uphyrkina, Olga; Smith, James L.; O’Brien, Stephen J.; Luo, Shu Jin

doi:10.1016/j.cub.2018.09.019

Cited by 83 publications

(152 citation statements)

References 63 publications

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“…Our results suggest a taxonomic re‐evaluation of the laingi subspecies may be appropriate, but this would likely depend in part on more detailed morphological analysis beyond the scope of the present paper. We note, however, that the subspecies concept is the subject of much debate, particularly in terms of how much subspecies taxonomy should depend on genetic clustering versus specific morphological traits contained in the initial subspecies description (Liu et al, ; Patten, ; Winker, ). Regardless of taxonomic treatment, we think the evidence in support of treating the Haida Gwaii population as a distinct conservation unit (e.g., a “designatable unit”) is strong: Haida Gwaii goshawks are very clearly genetically distinct, have a recognized phenotype (darker plumage than elsewhere, even compared to those in southeast Alaska and Vancouver Island), and inhabit an ecologically differentiated and geographically separated archipelago.…”

Section: Discussionmentioning

confidence: 99%

Population genomic analyses reveal a highly differentiated and endangered genetic cluster of northern goshawks (Accipiter gentilis laingi) in Haida Gwaii

Geraldes

Askelson

Nikelski

et al. 2019

Evolutionary Applications

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Accurate knowledge of geographic ranges and genetic relationships among populations is important when managing a species or population of conservation concern. Along the western coast of Canada, a subspecies of the northern goshawk ( Accipiter gentilis laingi ) is legally designated as Threatened. The range and distinctness of this form, in comparison with the broadly distributed North American subspecies ( Accipiter gentilis atricapillus ), is unclear. Given this morphological uncertainty, we analyzed genomic relationships in thousands of single nucleotide polymorphisms identified using genotyping‐by‐sequencing of high‐quality genetic samples. Results revealed a genetically distinct population of northern goshawks on the archipelago of Haida Gwaii and subtle structuring among other North American sampling regions. We then developed genotyping assays for ten loci that are highly differentiated between the two main genetic clusters, allowing inclusion of hundreds of low‐quality samples and confirming that the distinct genetic cluster is restricted to Haida Gwaii. As the laingi form was originally described as being based on Haida Gwaii (where the type specimen is from), further morphological analysis may result in this name being restricted to the Haida Gwaii genetic cluster. Regardless of taxonomic treatment, the distinct Haida Gwaii genetic cluster along with the small and declining population size of the Haida Gwaii population suggests a high risk of extinction of an ecologically and genetically distinct form of northern goshawk. Outside of Haida Gwaii, sampling regions along the coast of BC and southeast Alaska (often considered regions inhabited by laingi ) show some subtle differentiation from other North American regions. These results will increase the effectiveness of conservation management of northern goshawks in northwestern North America. More broadly, other conservation‐related studies of genetic variation may benefit from the two‐step approach we employed that first surveys genomic variation using high‐quality samples and then genotypes low‐quality samples at particularly informative loci.

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Section: Discussionmentioning

confidence: 99%

Population genomic analyses reveal a highly differentiated and endangered genetic cluster of northern goshawks (Accipiter gentilis laingi) in Haida Gwaii

Geraldes

Askelson

Nikelski

et al. 2019

Evolutionary Applications

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“…New species discoveries, as outlined above, plus genetic-based categorizations of subspecies also informed wildlife conservation units. For example, the definition of explicit tiger subspecies has confirmed the historically separated units of tiger conservation, as well as the postulated founder effect for today's tigers caused by the Toba volcanic explosion in Southeast Asia ∼73,000 years ago (78,79). Subspecies verification also happened with leopards, pumas, tigers, and lions (77)(78)(79)(80)(81).…”

Section: Genetics Of Endangered Speciesmentioning

confidence: 76%

“…For example, the definition of explicit tiger subspecies has confirmed the historically separated units of tiger conservation, as well as the postulated founder effect for today's tigers caused by the Toba volcanic explosion in Southeast Asia ∼73,000 years ago (78,79). Subspecies verification also happened with leopards, pumas, tigers, and lions (77)(78)(79)(80)(81). Population genetic and coalescent dating approaches allowed us to pinpoint the timing of historic demographic events like the cheetah and Florida panther bottlenecks (12,000 years ago around the end of the last ice age for cheetahs and a few hundred years ago for the Florida panther owing to deliberate decimation) (60,(71)(72)(73)(74)80).…”

Section: Genetics Of Endangered Speciesmentioning

confidence: 82%

“…The restoration program was a dramatic success, resulting in rapid recovery of population numbers, tripling of population size and density, and a measurable increase in fitness for the subspecies intercross offspring (74). Similar genetic reduction and restoration proposals have been offered, but never implemented, for Asian lions, Amur leopards, Amur tigers from the Russian Far East, and California Channel Island foxes (75)(76)(77)(78).…”

Section: Genetics Of Endangered Speciesmentioning

confidence: 99%

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A Beautiful Life: High Risk–High Payoff in Genetic Science

O’Brien

2020

Annu. Rev. Anim. Biosci.

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Portrait by Varvara Simonov n a aAnnu. Rev. Anim. Biosci. 2020.8:1-24. Downloaded from www.annualreviews.org Access provided by 50.80.253.90 on 03/16/20. For personal use only. AbstractThis narrative is a personal view of adventures in genetic science and society that have blessed my life and career across five decades. The advances I enjoyed and the lessons I learned derive from educational training, substantial collaboration, and growing up in the genomics age. I parse the stories into six research disciplines my students, fellows, and colleagues have entered and, in some cases, made an important difference. The first is comparative genetics, where evolutionary inference is applied to genome organization, from building gene maps in the 1970s to building whole genome sequences today. The second area tracks the progression of molecular evolutionary advances and applications to resolve the hierarchical relationship among living species in the silence of prehistory. The third endeavor outlines the birth and maturation of genetic studies and application to species conservation. The fourth theme discusses how emerging viruses studied in a genomic sense opened our eyes to host-pathogen interaction and interdependence. The fifth research emphasis outlines the population genetic-based search and discovery of human restriction genes that influence the epidemiological outcome of abrupt outbreaks, notably HIV-AIDS and several cancers. Finally, the last arena explored illustrates how genetic individualization in human and animals has improved forensic evidence in capital crimes. Each discipline has intuitive and technological overlaps, and each has benefitted from the contribution of genetic and genomic principles I learned so long ago from Drosophila. The journey continues.It's a very ancient saying but a true and honest thought, that if you become a teacher, by your pupils you'll be taught.-Oscar Hammerstein II, The King and I (1951) self-trained radio engineer. He began by building crystal radio sets in the late 1920s, and with but a high school diploma, he went on to build the CBS radio station and then the TV station in Rochester, where he became chief engineer. In my early youth, I paid little attention to science, being more interested in baseball, dogs, and rock and roll. My family relocated to Bethesda, Maryland, outside Washington, DC, in 1958, where I had a rather undistinguished high school performance that, to be frank, would limit my college admission opportunities. One thing I did enjoy in that period was singing and dancing in amateur high school musicals. Looking back, I suspect that these on-stage appearances provided terrific preparation in building confidence for public speaking later in the science arena. After hitchhiking 12 miles each day to Good Counsel High School in Wheaton, Maryland, I was excited to enter St. Francis College, a small liberal arts Catholic school run by Franciscan friars in the hills of western Pennsylvania. St. Francis was good for me. It protected me from my adolescent instinc...

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“…Whole genome sequences have helped in discovering disease‐causing and protective alleles (Epstein et al, 2016; Murchison et al, 2012), estimating inbreeding (Kardos et al, 2018) and low genetic variation (Abascal et al, 2016), planning and measuring success of genetic rescues (Saremi et al, 2018), estimating demographic history (Palkopoulou et al, 2015; Xue et al, 2015), ascertaining management units (Liu et al, 2018), and development of tools for several applications including monitoring populations (Faivre‐Rampant et al, 2016). Having noninvasive samples that can be used for whole genome sequencing will be an advantage for endangered species research as it may lead faster turnaround time.…”

Section: Discussionmentioning

confidence: 99%

Are shed hair genomes the most effective noninvasive resource for estimating relationships in the wild?

Khan

Patel

Bhattacharjee

et al. 2020

Ecology and Evolution

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Knowledge of relationships in wild populations is critical for better understanding mating systems and inbreeding scenarios to inform conservation strategies for endangered species. To delineate pedigrees in wild populations, study genetic connectivity, study genotype‐phenotype associations, trace individuals, or track wildlife trade, many identified individuals need to be genotyped at thousands of loci, mostly from noninvasive samples. This requires us to (a) identify the most common noninvasive sample available from identified individuals, (b) assess the ability to acquire genome‐wide data from such samples, and (c) evaluate the quality of such genome‐wide data, and its ability to reconstruct relationships between animals within a population. We followed identified individuals from a wild endangered tiger population and found that shed hair samples were the most common compared to scat samples, opportunistically found carcasses, and opportunistic invasive samples. We extracted DNA from these samples, prepared whole genome sequencing libraries, and sequenced genomes from these. Whole genome sequencing methods resulted in between 25%–98% of the genome sequenced for five such samples. Exploratory population genetic analyses revealed that these data were free of holistic biases and could recover expected population structure and relatedness. Mitochondrial genomes recovered matrilineages in accordance with long‐term monitoring data. Even with just five samples, we were able to uncover the matrilineage for three individuals with unknown ancestry. In summary, we demonstrated that noninvasive shed hair samples yield adequate quality and quantity of DNA in conjunction with sensitive library preparation methods, and provide reliable data from hundreds of thousands of SNPs across the genome. This makes shed hair an ideal noninvasive resource for studying individual‐based genetics of elusive endangered species in the wild.

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Genome-Wide Evolutionary Analysis of Natural History and Adaptation in the World’s Tigers

Cited by 83 publications

References 63 publications

Population genomic analyses reveal a highly differentiated and endangered genetic cluster of northern goshawks (Accipiter gentilis laingi) in Haida Gwaii

Population genomic analyses reveal a highly differentiated and endangered genetic cluster of northern goshawks (Accipiter gentilis laingi) in Haida Gwaii

A Beautiful Life: High Risk–High Payoff in Genetic Science

Are shed hair genomes the most effective noninvasive resource for estimating relationships in the wild?

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