1
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McComish BJ, Charleston MA, Parks M, Baroni C, Salvatore MC, Li R, Zhang G, Millar CD, Holland BR, Lambert DM. Ancient and Modern Genomes Reveal Microsatellites Maintain a Dynamic Equilibrium Through Deep Time. Genome Biol Evol 2024; 16:evae017. [PMID: 38412309 PMCID: PMC10972684 DOI: 10.1093/gbe/evae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 12/22/2023] [Accepted: 01/23/2024] [Indexed: 02/29/2024] Open
Abstract
Microsatellites are widely used in population genetics, but their evolutionary dynamics remain poorly understood. It is unclear whether microsatellite loci drift in length over time. This is important because the mutation processes that underlie these important genetic markers are central to the evolutionary models that employ microsatellites. We identify more than 27 million microsatellites using a novel and unique dataset of modern and ancient Adélie penguin genomes along with data from 63 published chordate genomes. We investigate microsatellite evolutionary dynamics over 2 timescales: one based on Adélie penguin samples dating to ∼46.5 ka and the other dating to the diversification of chordates aged more than 500 Ma. We show that the process of microsatellite allele length evolution is at dynamic equilibrium; while there is length polymorphism among individuals, the length distribution for a given locus remains stable. Many microsatellites persist over very long timescales, particularly in exons and regulatory sequences. These often retain length variability, suggesting that they may play a role in maintaining phenotypic variation within populations.
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Affiliation(s)
- Bennet J McComish
- School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7001, Australia
| | | | - Matthew Parks
- Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD 4111, Australia
- Department of Biology, University of Central Oklahoma, Edmond, OK 73034, USA
| | - Carlo Baroni
- Dipartimento di Scienze della Terra, University of Pisa, Pisa, Italy
- CNR-IGG, Institute of Geosciences and Earth Resources, Pisa, Italy
| | - Maria Cristina Salvatore
- Dipartimento di Scienze della Terra, University of Pisa, Pisa, Italy
- CNR-IGG, Institute of Geosciences and Earth Resources, Pisa, Italy
| | - Ruiqiang Li
- Novogene Bioinformatics Technology Co. Ltd., Beijing 100083, China
| | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
- Department of Biology, Centre for Social Evolution, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Craig D Millar
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Barbara R Holland
- School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia
| | - David M Lambert
- Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD 4111, Australia
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2
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Patel S, Evans CW, Stuckey A, Matzke NJ, Millar CD. A Unique Mitochondrial Gene Block Inversion in Antarctic Trematomin Fishes: A Cautionary Tale. J Hered 2022; 113:414-420. [PMID: 35657776 PMCID: PMC9308043 DOI: 10.1093/jhered/esac028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/29/2022] [Indexed: 11/29/2022] Open
Abstract
Many Antarctic notothenioid fishes have major rearrangements in their mitochondrial (mt) genomes. Here, we report the complete mt genomes of 3 trematomin notothenioids: the bald notothen (Trematomus (Pagothenia) borchgrevinki), the spotted notothen (T. nicolai), and the emerald notothen (T. bernacchii). The 3 mt genomes were sequenced using next-generation Illumina technology, and the assemblies verified by Sanger sequencing. When compared with the canonical mt gene order of the Antarctic silverfish (Pleuragramma antarctica), we found a large gene inversion in the 3 trematomin mt genomes that included tRNAIle, ND1, tRNALeu2, 16S, tRNAVal, 12S, tRNAPhe, and the control region. The trematomin mt genomes contained 3 intergenic spacers, which are thought to be the remnants of previous gene and control region duplications. All control regions included the characteristic conserved regulatory sequence motifs. Although short-read next-generation DNA sequencing technology has allowed the rapid and cost-effective sequencing of a large number of complete mt genomes, it is essential in all cases to verify the assembly in order to prevent the publication and use of erroneous data.
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Affiliation(s)
- Selina Patel
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Clive W Evans
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Alex Stuckey
- Genomics England, Queen Mary University of London, Dawson Hall, London EC1M 6BQ, United Kingdom
| | - Nicholas J Matzke
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Craig D Millar
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
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3
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Lee KD, Millar CD, Brekke P, Whibley A, Ewen JG, Hingston M, Zhu A, Santure AW. The design and application of a 50 K SNP chip for a threatened Aotearoa New Zealand passerine, the hihi. Mol Ecol Resour 2021; 22:415-429. [PMID: 34323011 DOI: 10.1111/1755-0998.13480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/30/2022]
Abstract
Next-generation sequencing has transformed the fields of ecological and evolutionary genetics by allowing for cost-effective identification of genome-wide variation. Single nucleotide polymorphism (SNP) arrays, or "SNP chips", enable very large numbers of individuals to be consistently genotyped at a selected set of these identified markers, and also offer the advantage of being able to analyse samples of variable DNA quality. We used reduced representation restriction-aided digest sequencing (RAD-seq) of 31 birds of the threatened hihi (Notiomystis cincta; stitchbird) and low-coverage whole genome sequencing (WGS) of 10 of these birds to develop an Affymetrix 50 K SNP chip. We overcame the limitations of having no hihi reference genome and a low quantity of sequence data by separate and pooled de novo assembly of each of the 10 WGS birds. Reads from all individuals were mapped back to these de novo assemblies to identify SNPs. A subset of RAD-seq and WGS SNPs were selected for inclusion on the chip, prioritising SNPs with the highest quality scores whose flanking sequence uniquely aligned to the zebra finch (Taeniopygia guttata) genome. Of the 58,466 SNPs manufactured on the chip, 72% passed filtering metrics and were polymorphic. By genotyping 1,536 hihi on the array, we found that SNPs detected in multiple assemblies were more likely to successfully genotype, representing a cost-effective approach to identify SNPs for genotyping. Here, we demonstrate the utility of the SNP chip by describing the high rates of linkage disequilibrium in the hihi genome, reflecting the history of population bottlenecks in the species.
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Affiliation(s)
- Kate D Lee
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Craig D Millar
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Regent's Park, London, UK
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - John G Ewen
- Institute of Zoology, Zoological Society of London, Regent's Park, London, UK
| | - Melanie Hingston
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Amy Zhu
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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4
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Schultz H, Chang K, Bury SJ, Gaskett AC, Dennis TE, Ismar-Rebitz SMH, Southey I, Hohnhold RJ, Millar CD. Sex-specific foraging of an apex predator puts females at risk of human-wildlife conflict. J Anim Ecol 2021; 90:1776-1786. [PMID: 33844849 DOI: 10.1111/1365-2656.13496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 03/30/2021] [Indexed: 11/29/2022]
Abstract
Urbanisation and anthropogenic alteration of ecosystems has led to conflict between humans and wildlife. Such conflict is often observed in apex predators. Although human-wildlife conflict has been extensively studied, male/female differences in behaviour are rarely considered. We investigated male/female differences in foraging behaviour of the predatory/scavenging brown skua Catharacta antarctica lonnbergi breeding on a New Zealand island nature reserve in proximity to farmland. These skuas are subject to culling, when perceived as a threat to livestock. As part of a long-term ecological study, we used high-resolution Global Positioning System (GPS) devices to characterise the space-use of foraging brown skuas. We also analysed stable isotopes of carbon (δ13 C) and nitrogen (δ15 N) from modern and archived blood samples to investigate possible changes in diet over the past ~30 years. Analysis of 100 GPS tracks collected from 2014 to 2016 demonstrated that males and females consistently visited different habitats. Males spent most of their time close to their breeding territory on the island nature reserve and females frequently visited a farmed island approximately two kilometres away. Consistent with this finding, we show that male and female skuas also differed markedly in their diets: males specialised on burrow-nesting white-faced storm petrels Pelagodroma marina (80%) with only a small proportion of sheep remains Ovis aries (<6%) contributing to their diet. In contrast, female diet comprised 27% white-faced storm petrels, other seabirds (18%) and a relatively large proportion of sheep remains (47%). Further, our data (186 blood samples from 122 individuals) show that this male/female difference in diet has persisted at least since 1987. Because females fed disproportionally on sheep remains, they may be more vulnerable to being culled by farmers. Importantly, our case study suggests that intersexual differences in diet and foraging patterns can have major implications for the reproduction and survival of apex predators that interact with farming. We strongly suggest that intersexual differences in behaviour should be considered when investigating human-wildlife conflicts.
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Affiliation(s)
- Hendrik Schultz
- School of Biological Sciences/Te Kura Mātauranga Koiora, The University of Auckland/Te Whare Wānanga o Tāmaki Makaurau, Auckland, New Zealand
| | - Kevin Chang
- School of Biological Sciences/Te Kura Mātauranga Koiora, The University of Auckland/Te Whare Wānanga o Tāmaki Makaurau, Auckland, New Zealand
| | - Sarah J Bury
- National Institute of Water and Atmospheric Research Ltd, Wellington, New Zealand
| | - Anne C Gaskett
- School of Biological Sciences/Te Kura Mātauranga Koiora, The University of Auckland/Te Whare Wānanga o Tāmaki Makaurau, Auckland, New Zealand
| | - Todd E Dennis
- Department of Biology, Fiji National University, Nasinu, Republic of Fiji
| | - Stefanie M H Ismar-Rebitz
- School of Biological Sciences/Te Kura Mātauranga Koiora, The University of Auckland/Te Whare Wānanga o Tāmaki Makaurau, Auckland, New Zealand.,GEOMAR Helmholtz-Centre for Ocean Research, Kiel, Germany
| | - Ian Southey
- Birds New Zealand, South Auckland Branch, New Zealand
| | - Rebecca J Hohnhold
- School of Biological Sciences/Te Kura Mātauranga Koiora, The University of Auckland/Te Whare Wānanga o Tāmaki Makaurau, Auckland, New Zealand
| | - Craig D Millar
- School of Biological Sciences/Te Kura Mātauranga Koiora, The University of Auckland/Te Whare Wānanga o Tāmaki Makaurau, Auckland, New Zealand
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5
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Yıldırım Y, Anderson MJ, Hansson B, Patel S, Millar CD, Rainey PB. Genetic structure of the grey side-gilled sea slug (Pleurobranchaea maculata) in coastal waters of New Zealand. PLoS One 2018; 13:e0202197. [PMID: 30114275 PMCID: PMC6095540 DOI: 10.1371/journal.pone.0202197] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 07/30/2018] [Indexed: 01/09/2023] Open
Abstract
Pleurobranchaea maculata is a rarely studied species of the Heterobranchia found throughout the south and western Pacific-and recently recorded in Argentina-whose population genetic structure is unknown. Interest in the species was sparked in New Zealand following a series of dog deaths caused by ingestions of slugs containing high levels of the neurotoxin tetrodotoxin. Here we describe the genetic structure and demographic history of P. maculata populations from five principle locations in New Zealand based on extensive analyses of 12 microsatellite loci and the COI and CytB regions of mitochondrial DNA (mtDNA). Microsatellite data showed significant differentiation between northern and southern populations with population structure being associated with previously described regional variations in tetrodotoxin concentrations. However, mtDNA sequence data did not support such structure, revealing a star-shaped haplotype network with estimates of expansion time suggesting a population expansion in the Pleistocene era. Inclusion of publicly available mtDNA sequence sea slugs from Argentina did not alter the star-shaped network. We interpret our data as indicative of a single founding population that fragmented following geographical changes that brought about the present day north-south divide in New Zealand waters. Lack of evidence of cryptic species supports data indicating that differences in toxicity of individuals among regions are a consequence of differences in diet.
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Affiliation(s)
- Yeşerin Yıldırım
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Marti J. Anderson
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
| | - Selina Patel
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Craig D. Millar
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Paul B. Rainey
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), CNRS UMR 8231, PSL Research University, Paris, France
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6
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Patel S, Thompson KF, Santure AW, Constantine R, Millar CD. Genetic Kinship Analyses Reveal That Gray's Beaked Whales Strand in Unrelated Groups. J Hered 2017; 108:456-461. [PMID: 28498990 DOI: 10.1093/jhered/esx021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 02/16/2017] [Indexed: 11/12/2022] Open
Abstract
Some marine mammals are so rarely seen that their life history and social structure remain a mystery. Around New Zealand, Gray's beaked whales (Mesoplodon grayi) are almost never seen alive, yet they are a commonly stranded species. Gray's are unique among the beaked whales in that they frequently strand in groups, providing an opportunity to investigate their social organization. We examined group composition and genetic kinship in 113 Gray's beaked whales with samples collected over a 20-year period. Fifty-six individuals stranded in 19 groups (2 or more individuals), and 57 whales stranded individually. Mitochondrial control region haplotypes and microsatellite genotypes (16 loci) were obtained for 103 whales. We estimated pairwise relatedness between all pairs of individuals and average relatedness within, and between, groups. We identified 6 mother-calf pairs and 2 half-siblings, including 2 whales in different strandings 17 years and 1500 km apart. Surprisingly, none of the adults stranding together were related suggesting that groups are not formed through the retention of kin. These data suggest that both sexes may disperse from their mothers, and groups consisting of unrelated subadults are common. We also found no instances of paternity within the groups. Our results provide the first insights into dispersal, social organization, and the mating system in this rarely sighted species. Why whales strand is still unknown but, in Gray's beaked whales, the dead can tell us much about the living.
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Affiliation(s)
- Selina Patel
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Kirsten F Thompson
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.,Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope, Stocker Road, Exeter EX4 4QD, UK
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Rochelle Constantine
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Craig D Millar
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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7
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Heupink TH, Subramanian S, Wright JL, Endicott P, Westaway MC, Huynen L, Parson W, Millar CD, Willerslev E, Lambert DM. Ancient mtDNA sequences from the First Australians revisited. Proc Natl Acad Sci U S A 2016; 113:6892-7. [PMID: 27274055 PMCID: PMC4922152 DOI: 10.1073/pnas.1521066113] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The publication in 2001 by Adcock et al. [Adcock GJ, et al. (2001) Proc Natl Acad Sci USA 98(2):537-542] in PNAS reported the recovery of short mtDNA sequences from ancient Australians, including the 42,000-y-old Mungo Man [Willandra Lakes Hominid (WLH3)]. This landmark study in human ancient DNA suggested that an early modern human mitochondrial lineage emerged in Asia and that the theory of modern human origins could no longer be considered solely through the lens of the "Out of Africa" model. To evaluate these claims, we used second generation DNA sequencing and capture methods as well as PCR-based and single-primer extension (SPEX) approaches to reexamine the same four Willandra Lakes and Kow Swamp 8 (KS8) remains studied in the work by Adcock et al. Two of the remains sampled contained no identifiable human DNA (WLH15 and WLH55), whereas the Mungo Man (WLH3) sample contained no Aboriginal Australian DNA. KS8 reveals human mitochondrial sequences that differ from the previously inferred sequence. Instead, we recover a total of five modern European contaminants from Mungo Man (WLH3). We show that the remaining sample (WLH4) contains ∼1.4% human DNA, from which we assembled two complete mitochondrial genomes. One of these was a previously unidentified Aboriginal Australian haplotype belonging to haplogroup S2 that we sequenced to a high coverage. The other was a contaminating modern European mitochondrial haplotype. Although none of the sequences that we recovered matched those reported by Adcock et al., except a contaminant, these findings show the feasibility of obtaining important information from ancient Aboriginal Australian remains.
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Affiliation(s)
- Tim H Heupink
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Sankar Subramanian
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Joanne L Wright
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Phillip Endicott
- Department of Zoology, Oxford University, Oxford OX1 2JD, United Kingdom
| | | | - Leon Huynen
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia
| | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, 6020 Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA 16801
| | - Craig D Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Eske Willerslev
- Centre for GeoGenetics, University of Copenhagen, 1017 Copenhagen, Denmark
| | - David M Lambert
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia;
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8
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Ludin NM, Cheeseman JF, Merry AF, Millar CD, Warman GR. The effects of the general anaesthetic isoflurane on the honey bee (Apis mellifera) circadian clock. Chronobiol Int 2016; 33:128-33. [PMID: 26730506 DOI: 10.3109/07420528.2015.1113987] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
General anaesthesia administered during the day has previously been shown to phase shift the honey bee clock. We describe a phase response curve for honey bees (n=105) to six hour isoflurane anaesthesia. The honey bee isoflurane PRC is "weak" with a delay portion (maximum shift of -1.88 hours, circadian time 0 - 3) but no advance zone. The isoflurane-induced shifts observed here are in direct opposition to those of light. Furthermore, concurrent administration of light and isoflurane abolishes the shifts that occur with isoflurane alone. Light may thus provide a means of reducing isoflurane-induced phase shifts.
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Affiliation(s)
- Nicola M Ludin
- a Department of Anaesthesiology, Faculty of Medical and Health Sciences , University of Auckland , Auckland , New Zealand
| | - James F Cheeseman
- a Department of Anaesthesiology, Faculty of Medical and Health Sciences , University of Auckland , Auckland , New Zealand
| | - Alan F Merry
- a Department of Anaesthesiology, Faculty of Medical and Health Sciences , University of Auckland , Auckland , New Zealand
| | - Craig D Millar
- a Department of Anaesthesiology, Faculty of Medical and Health Sciences , University of Auckland , Auckland , New Zealand.,b Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, Faculty of Science , University of Auckland , Auckland , New Zealand
| | - Guy R Warman
- a Department of Anaesthesiology, Faculty of Medical and Health Sciences , University of Auckland , Auckland , New Zealand
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9
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Thompson KF, Patel S, Baker CS, Constantine R, Millar CD. Bucking the trend: genetic analysis reveals high diversity, large population size and low differentiation in a deep ocean cetacean. Heredity (Edinb) 2015; 116:277-85. [PMID: 26626574 DOI: 10.1038/hdy.2015.99] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 10/02/2015] [Accepted: 10/05/2015] [Indexed: 11/09/2022] Open
Abstract
Understanding the genetic structure of a population is essential to its conservation and management. We report the level of genetic diversity and determine the population structure of a cryptic deep ocean cetacean, the Gray's beaked whale (Mesoplodon grayi). We analysed 530 bp of mitochondrial control region and 12 microsatellite loci from 94 individuals stranded around New Zealand and Australia. The samples cover a large area of the species distribution (~6000 km) and were collected over a 22-year period. We show high genetic diversity (h=0.933-0.987, π=0.763-0.996% and Rs=4.22-4.37, He=0.624-0.675), and, in contrast to other cetaceans, we found a complete lack of genetic structure in both maternally and biparentally inherited markers. The oceanic habitats around New Zealand are diverse with extremely deep waters, seamounts and submarine canyons that are suitable for Gray's beaked whales and their prey. We propose that the abundance of this rich habitat has promoted genetic homogeneity in this species. Furthermore, it has been suggested that the lack of beaked whale sightings is the result of their low abundance, but this is in contrast to our estimates of female effective population size based on mitochondrial data. In conclusion, the high diversity and lack of genetic structure can be explained by a historically large population size, in combination with no known exploitation, few apparent behavioural barriers and abundant habitat.
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Affiliation(s)
- K F Thompson
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,The Allan Wilson Centre, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - S Patel
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,The Allan Wilson Centre, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - C S Baker
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Department of Fisheries and Wildlife and Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - R Constantine
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - C D Millar
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,The Allan Wilson Centre, School of Biological Sciences, University of Auckland, Auckland, New Zealand
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10
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Parks M, Subramanian S, Baroni C, Salvatore MC, Zhang G, Millar CD, Lambert DM. Ancient population genomics and the study of evolution. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130381. [PMID: 25487332 DOI: 10.1098/rstb.2013.0381] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recently, the study of ancient DNA (aDNA) has been greatly enhanced by the development of second-generation DNA sequencing technologies and targeted enrichment strategies. These developments have allowed the recovery of several complete ancient genomes, a result that would have been considered virtually impossible only a decade ago. Prior to these developments, aDNA research was largely focused on the recovery of short DNA sequences and their use in the study of phylogenetic relationships, molecular rates, species identification and population structure. However, it is now possible to sequence a large number of modern and ancient complete genomes from a single species and thereby study the genomic patterns of evolutionary change over time. Such a study would herald the beginnings of ancient population genomics and its use in the study of evolution. Species that are amenable to such large-scale studies warrant increased research effort. We report here progress on a population genomic study of the Adélie penguin (Pygoscelis adeliae). This species is ideally suited to ancient population genomic research because both modern and ancient samples are abundant in the permafrost conditions of Antarctica. This species will enable us to directly address many of the fundamental questions in ecology and evolution.
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Affiliation(s)
- M Parks
- Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - S Subramanian
- Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - C Baroni
- Dipartimento di Scienze della Terra, Universita di Pisa, Pisa, Italy
| | - M C Salvatore
- Dipartimento di Scienze della Terra, Universita di Pisa, Pisa, Italy
| | - G Zhang
- China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, Republic of China Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - C D Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - D M Lambert
- Environmental Futures Research Institute, Griffith University, Nathan, Australia
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11
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Subramanian S, Mohandesan E, Millar CD, Lambert DM. Distance-dependent patterns of molecular divergences in Tuatara mitogenomes. Sci Rep 2015; 5:8703. [PMID: 25731894 PMCID: PMC4346810 DOI: 10.1038/srep08703] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 02/02/2015] [Indexed: 01/21/2023] Open
Abstract
Population genetic models predict that populations that are geographically close to each other are expected to be genetically more similar to each other compared to those that are widely separate. However the patterns of relationships between geographic distance and molecular divergences at neutral and constrained regions of the genome are unclear. We attempted to clarify this relationship by sequencing complete mitochondrial genomes of the relic species Tuatara (Sphenodon punctatus) from ten offshore islands of New Zealand. We observed a positive relationship that showed a proportional increase in the neutral diversity at synonymous sites (dS), with increasing geographical distance. In contrast we showed that diversity at evolutionarily constrained sites (dC) was elevated in the case of comparisons involving closely located populations. Conversely diversity was reduced in the case of comparisons between distantly located populations. These patterns were confirmed by a significant negative relationship between the ratio of dC/dS and geographic distance. The observed high dC/dS could be explained by the abundance of deleterious mutations in comparisons involving closely located populations, due to the recent population divergence times. Since distantly related populations were separated over long periods of time, deleterious mutations might have been removed by purifying selection.
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Affiliation(s)
- Sankar Subramanian
- Enviromental Futures Research Institute, Griffith University, Nathan 4111, Australia
| | - Elmira Mohandesan
- Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, New Zealand
| | - Craig D Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Private 92019, Auckland, New Zealand
| | - David M Lambert
- Enviromental Futures Research Institute, Griffith University, Nathan 4111, Australia
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Li C, Zhang Y, Li J, Kong L, Hu H, Pan H, Xu L, Deng Y, Li Q, Jin L, Yu H, Chen Y, Liu B, Yang L, Liu S, Zhang Y, Lang Y, Xia J, He W, Shi Q, Subramanian S, Millar CD, Meader S, Rands CM, Fujita MK, Greenwold MJ, Castoe TA, Pollock DD, Gu W, Nam K, Ellegren H, Ho SYW, Burt DW, Ponting CP, Jarvis ED, Gilbert MTP, Yang H, Wang J, Lambert DM, Wang J, Zhang G. Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment. Gigascience 2014; 3:27. [PMID: 25671092 PMCID: PMC4322438 DOI: 10.1186/2047-217x-3-27] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 11/06/2014] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adélie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri]. RESULTS Phylogenetic dating suggests that early penguins arose ~60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from ~1 million years ago to ~100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology. CONCLUSIONS Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment.
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Affiliation(s)
- Cai Li
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
- />Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Yong Zhang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Jianwen Li
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Lesheng Kong
- />MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX UK
| | - Haofu Hu
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Hailin Pan
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Luohao Xu
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Yuan Deng
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Qiye Li
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
- />Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Lijun Jin
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Hao Yu
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Yan Chen
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Binghang Liu
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Linfeng Yang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Shiping Liu
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Yan Zhang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Yongshan Lang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Jinquan Xia
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Weiming He
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Qiong Shi
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Sankar Subramanian
- />Environmental Futures Centre, Griffith University, Nathan, QLD 4111 Australia
| | - Craig D Millar
- />Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Stephen Meader
- />MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX UK
| | - Chris M Rands
- />MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX UK
| | - Matthew K Fujita
- />MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX UK
- />Department of Biology, University of Texas at Arlington, Arlington, TX 76019 USA
| | - Matthew J Greenwold
- />Department of Biological Sciences, University of South Carolina, Columbia, SC USA
| | - Todd A Castoe
- />Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045 USA
- />Biology Department, University of Texas Arlington, Arlington, TX 76016 USA
| | - David D Pollock
- />Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO 80045 USA
| | - Wanjun Gu
- />Research Centre of Learning Sciences, Southeast University, Nanjing, 210096 China
| | - Kiwoong Nam
- />Department of Evolutionary Biology, Uppsala University, Norbyvagen 18D, SE-752 36 Uppsala, Sweden
- />Bioinformatics Research Centre (BiRC), Aarhus University, C.F.Møllers Allé 8, 8000 Aarhus C, Denmark
| | - Hans Ellegren
- />Department of Evolutionary Biology, Uppsala University, Norbyvagen 18D, SE-752 36 Uppsala, Sweden
| | - Simon YW Ho
- />School of Biological Sciences, University of Sydney, Sydney, NSW 2006 Australia
| | - David W Burt
- />Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus Midlothian, Edinburgh, EH25 9RG UK
| | - Chris P Ponting
- />MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX UK
| | - Erich D Jarvis
- />Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC27710 USA
| | - M Thomas P Gilbert
- />Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- />Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, WA 6102 Australia
| | - Huanming Yang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
- />Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Jian Wang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - David M Lambert
- />Environmental Futures Centre, Griffith University, Nathan, QLD 4111 Australia
| | - Jun Wang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
- />Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
- />Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
- />Macau University of Science and Technology, Avenida Wai long, Taipa, Macau, 999078 China
- />Department of Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Guojie Zhang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
- />Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen, DK-2100 Denmark
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Yıldırım Y, Patel S, Millar CD, Rainey PB. Microsatellite development for a tetrodotoxin-containing sea slug (Pleurobranchaea maculata). BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Huynen L, Suzuki T, Ogura T, Watanabe Y, Millar CD, Hofreiter M, Smith C, Mirmoeini S, Lambert DM. Reconstruction and in vivo analysis of the extinct tbx5 gene from ancient wingless moa (Aves: Dinornithiformes). BMC Evol Biol 2014; 14:75. [PMID: 24885927 PMCID: PMC4101845 DOI: 10.1186/1471-2148-14-75] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 03/25/2014] [Indexed: 12/16/2022] Open
Abstract
Background The forelimb-specific gene tbx5 is highly conserved and essential for the development of forelimbs in zebrafish, mice, and humans. Amongst birds, a single order, Dinornithiformes, comprising the extinct wingless moa of New Zealand, are unique in having no skeletal evidence of forelimb-like structures. Results To determine the sequence of tbx5 in moa, we used a range of PCR-based techniques on ancient DNA to retrieve all nine tbx5 exons and splice sites from the giant moa, Dinornis. Moa Tbx5 is identical to chicken Tbx5 in being able to activate the downstream promotors of fgf10 and ANF. In addition we show that missexpression of moa tbx5 in the hindlimb of chicken embryos results in the formation of forelimb features, suggesting that Tbx5 was fully functional in wingless moa. An alternatively spliced exon 1 for tbx5 that is expressed specifically in the forelimb region was shown to be almost identical between moa and ostrich, suggesting that, as well as being fully functional, tbx5 is likely to have been expressed normally in moa since divergence from their flighted ancestors, approximately 60 mya. Conclusions The results suggests that, as in mice, moa tbx5 is necessary for the induction of forelimbs, but is not sufficient for their outgrowth. Moa Tbx5 may have played an important role in the development of moa’s remnant forelimb girdle, and may be required for the formation of this structure. Our results further show that genetic changes affecting genes other than tbx5 must be responsible for the complete loss of forelimbs in moa.
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Affiliation(s)
| | | | | | | | | | | | | | | | - David M Lambert
- Environmental Futures Centre, Griffith University, 170 Kessels Road, Nathan Qld 4111, Australia.
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15
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Chambers GK, Curtis C, Millar CD, Huynen L, Lambert DM. DNA fingerprinting in zoology: past, present, future. Investig Genet 2014; 5:3. [PMID: 24490906 PMCID: PMC3909909 DOI: 10.1186/2041-2223-5-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 12/19/2013] [Indexed: 01/07/2023]
Abstract
In 1962, Thomas Kuhn famously argued that the progress of scientific knowledge results from periodic 'paradigm shifts' during a period of crisis in which new ideas dramatically change the status quo. Although this is generally true, Alec Jeffreys' identification of hypervariable repeat motifs in the human beta-globin gene, and the subsequent development of a technology known now as 'DNA fingerprinting', also resulted in a dramatic shift in the life sciences, particularly in ecology, evolutionary biology, and forensics. The variation Jeffreys recognized has been used to identify individuals from tissue samples of not just humans, but also of many animal species. In addition, the technology has been used to determine the sex of individuals, as well as paternity/maternity and close kinship. We review a broad range of such studies involving a wide diversity of animal species. For individual researchers, Jeffreys' invention resulted in many ecologists and evolutionary biologists being given the opportunity to develop skills in molecular biology to augment their whole organism focus. Few developments in science, even among the subsequent genome discoveries of the 21st century, have the same wide-reaching significance. Even the later development of PCR-based genotyping of individuals using microsatellite repeats sequences, and their use in determining multiple paternity, is conceptually rooted in Alec Jeffreys' pioneering work.
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Affiliation(s)
| | | | | | | | - David M Lambert
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia.
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16
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Thompson KF, Patel S, Williams L, Tsai P, Constantine R, Baker CS, Millar CD. High coverage of the complete mitochondrial genome of the rare Gray's beaked whale (Mesoplodon grayi) using Illumina next generation sequencing. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:128-9. [PMID: 24450706 DOI: 10.3109/19401736.2013.878908] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Using an Illumina platform, we shot-gun sequenced the complete mitochondrial genome of Gray's beaked whale (Mesoplodon grayi) to an average coverage of 152X. We performed a de novo assembly using SOAPdenovo2 and determined the total mitogenome length to be 16,347 bp. The nucleotide composition was asymmetric (33.3% A, 24.6% C, 12.6% G, 29.5% T) with an overall GC content of 37.2%. The gene organization was similar to that of other cetaceans with 13 protein-coding genes, 2 rRNAs (12S and 16S), 22 predicted tRNAs and 1 control region or D-loop. We found no evidence of heteroplasmy or nuclear copies of mitochondrial DNA in this individual. Beaked whales within the genus Mesoplodon are rarely seen at sea and their basic biology is poorly understood. These data will contribute to resolving the phylogeography and population ecology of this speciose group.
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Affiliation(s)
- Kirsten F Thompson
- a The Allan Wilson Centre, School of Biological Sciences, University of Auckland , Auckland , New Zealand .,b School of Biological Sciences, University of Auckland , Auckland , New Zealand , and
| | - Selina Patel
- a The Allan Wilson Centre, School of Biological Sciences, University of Auckland , Auckland , New Zealand .,b School of Biological Sciences, University of Auckland , Auckland , New Zealand , and
| | - Liam Williams
- b School of Biological Sciences, University of Auckland , Auckland , New Zealand , and
| | - Peter Tsai
- b School of Biological Sciences, University of Auckland , Auckland , New Zealand , and
| | - Rochelle Constantine
- b School of Biological Sciences, University of Auckland , Auckland , New Zealand , and
| | - C Scott Baker
- b School of Biological Sciences, University of Auckland , Auckland , New Zealand , and.,c Department of Fisheries and Wildlife and Marine Mammal Institute , Oregon State University , Newport , OR , USA
| | - Craig D Millar
- a The Allan Wilson Centre, School of Biological Sciences, University of Auckland , Auckland , New Zealand .,b School of Biological Sciences, University of Auckland , Auckland , New Zealand , and
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Abstract
Penguins are a remarkable group of birds, with the 18 extant species living in diverse climatic zones from the tropics to Antarctica. The timing of the origin of these extant penguins remains controversial. Previous studies based on DNA sequences and fossil records have suggested widely differing times for the origin of the group. This has given rise to widely differing biogeographic narratives about their evolution. To resolve this problem, we sequenced five introns from 11 species representing all genera of living penguins. Using these data and other available DNA sequences, together with the ages of multiple penguin fossils to calibrate the molecular clock, we estimated the age of the most recent common ancestor of extant penguins to be 20.4 Myr (17.0-23.8 Myr). This time is half of the previous estimates based on molecular sequence data. Our results suggest that most of the major groups of extant penguins diverged 11-16 Ma. This overlaps with the sharp decline in Antarctic temperatures that began approximately 12 Ma, suggesting a possible relationship between climate change and penguin evolution.
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18
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Abstract
Tuatara are the sister taxon to the Squamata (including lizards and snakes) and are regarded as the most distinctive surviving reptilian genus. They are currently inhabits on offshore islands around New Zealand and have been recognized as a species in need of active conservation management. In this study, we report a total number of five nearly complete mitochondrial genomes, which were sequenced by Sanger and Next Generation DNA sequencing methods. Our phylogenomic analysis revealed distinct clustering of tuatara populations from the north and south islands of New Zealand.
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Affiliation(s)
- Elmira Mohandesan
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland , Auckland , New Zealand and
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19
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Abstract
During the summer months, Adélie penguins represent the dominant biomass of terrestrial Antarctica. Literally millions of individuals nest in ice-free areas around the coast of the continent. Hence, these modern populations of Adélie penguins have often been championed as an ideal biological indicator of ecological and environmental changes that we currently face. In addition, Adélie penguins show an extraordinary record of sub-fossil remains, dating back to the late Pleistocene. At this time, temperatures were much lower than now. Hence, this species offers unique long-term information, at both the genomic and ecological levels, about how a species has responded to climate change over more than 40 000 years.
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Affiliation(s)
- Craig D Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, New Zealand
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20
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Abstract
Recently two developments have had a major impact on the field of ancient DNA (aDNA). First, new advances in DNA sequencing, in combination with improved capture/enrichment methods, have resulted in the recovery of orders of magnitude more DNA sequence data from ancient animals. Second, there has been an increase in the range of tissue types employed in aDNA. Hair in particular has proven to be very successful as a source of DNA because of its low levels of contamination and high level of ancient endogenous DNA. These developments have resulted in significant advances in our understanding of recently extinct animals: namely their evolutionary relationships, physiology, and even behaviour. Hair has been used to recover the first complete ancient nuclear genome, that of the extinct woolly mammoth, which then facilitated the expression and functional analysis of haemoglobins. Finally, we speculate on the consequences of these developments for the possibility of recreating extinct animals.
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Affiliation(s)
- Leon Huynen
- Griffith School of Environment and the School of Biomolecular and Physical Sciences, Griffith University, Nathan, Australia
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Abstract
The authors report a phase response curve (PRC) for individual honey bees (Apis mellifera) to single 1-h light pulses (1000 lux) using an Aschoff Type 1 protocol (n = 134). The bee PRC is a weak (Type 1) PRC with a maximum advance of 1.5 h between circadian time (CT) 18 and 3 and a maximum delay of 1.5 h between CT 12 and 18. This is the first published honey bee light PRC and provides an important resource for chronobiologists and honey bee researchers. It may also have practical applications for what is an economically important species frequently transported across different time zones.
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Affiliation(s)
- Nicola M Ludin
- Department of Anaesthesiology, Faculty of Medical and Health Sciences, University of Auckland, New Zealand
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22
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Abstract
While flying remains one of the safest means of travel, reported birdstrikes on aircraft have risen. This is a result of increased aircraft flight movements, changes in agricultural methods and greater environmental awareness contributing to growing populations of hazardous bird species, as well as more diligent reporting of incidents. Measures to mitigate this hazard require accurate data about the species involved; however, the remains of birds from these incidents are often not easy to identify. Reported birdstrikes include a substantial number where the species cannot be determined from morphology alone. DNA barcoding offers a reliable method of identifying species from very small amounts of organic material such as blood, muscle and feathers. We compare species identification based on morphological criteria and identifications based on mitochondrial cytochrome c oxidase subunit I DNA barcoding methods for New Zealand species. Our data suggest that DNA-based identification can substantially add to the accuracy of species identifications, and these methods represent an important addition to existing procedures to improve air safety. In addition, we outline simple and effective protocols for the recovery and processing of samples for DNA barcoding.
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Affiliation(s)
- John Waugh
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Natural Sciences, Massey University, Private Bag 102 904, NSMC, Auckland, New Zealand.
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23
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Abstract
Feather cloaks ("kakahu"), particularly those adorned with kiwi feathers, are treasured items or "taonga" to the Māori people of "Aotearoa"/New Zealand. They are considered iconic expression of Māori culture. Despite their status, much of our knowledge of the materials used to construct cloaks, the provenance of cloaks, and the origins of cloak making itself, has been lost. We used ancient DNA methods to recover mitochondrial DNA sequences from 849 feather samples taken from 109 cloaks. We show that almost all (>99%) of the cloaks were constructed using feathers from North Island brown kiwi. Molecular sexing of nuclear DNA recovered from 92 feather cloak samples also revealed that the sex ratio of birds deviated from a ratio of 1:1 observed in reference populations. Additionally, we constructed a database of 185 mitochondrial control region DNA sequences of kiwi feathers comprising samples collected from 26 North Island locations together with data available from the literature. Genetic subdivision (G(ST)), nucleotide subdivision (N(ST)) and Spatial Analysis of Molecular Variants (SAMOVA) analyses revealed high levels of genetic structuring in North Island brown kiwi. Together with sequence data from previously studied ancient and modern kiwi samples, we were able to determine the geographic provenance of 847 cloak feathers from 108 cloaks. A surprising proportion (15%) of cloaks were found to contain feathers from different geographic locations, providing evidence of kiwi trading among Māori tribes or organized hunting trips into other tribal areas. Our data also suggest that the east of the North Island of New Zealand was the most prolific of all kiwi cloak making areas, with over 50% of all cloaks analyzed originating from this region. Similar molecular approaches have the potential to discover a wealth of lost information from artifacts of endemic cultures worldwide.
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Affiliation(s)
- K Hartnup
- Institute of Natural Sciences, Massey University, Auckland, New Zealand
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Subramanian S, Huynen L, Millar CD, Lambert DM. Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi. BMC Evol Biol 2010; 10:387. [PMID: 21156082 PMCID: PMC3009673 DOI: 10.1186/1471-2148-10-387] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 12/15/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Kiwi is a highly distinctive, flightless and endangered ratite bird endemic to New Zealand. To understand the patterns of molecular evolution of the nuclear protein-coding genes in brown kiwi (Apteryx australis mantelli) and to determine the timescale of avian history we sequenced a transcriptome obtained from a kiwi embryo using next generation sequencing methods. We then assembled the conserved protein-coding regions using the chicken proteome as a scaffold. RESULTS Using 1,543 conserved protein coding genes we estimated the neutral evolutionary divergence between the kiwi and chicken to be ~45%, which is approximately equal to the divergence computed for the human-mouse pair using the same set of genes. A large fraction of genes was found to be under high selective constraint, as most of the expressed genes appeared to be involved in developmental gene regulation. Our study suggests a significant relationship between gene expression levels and protein evolution. Using sequences from over 700 nuclear genes we estimated the divergence between the two basal avian groups, Palaeognathae and Neognathae to be 132 million years, which is consistent with previous studies using mitochondrial genes. CONCLUSIONS The results of this investigation revealed patterns of mutation and purifying selection in conserved protein coding regions in birds. Furthermore this study suggests a relatively cost-effective way of obtaining a glimpse into the fundamental molecular evolutionary attributes of a genome, particularly when no closely related genomic sequence is available.
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Affiliation(s)
- Sankar Subramanian
- Griffith School of Environment and the School of Biomolecular and Physical Sciences, Griffith University, 170 Kessels Road, Nathan, Qld 4111 Australia
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
| | - Leon Huynen
- Griffith School of Environment and the School of Biomolecular and Physical Sciences, Griffith University, 170 Kessels Road, Nathan, Qld 4111 Australia
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
| | - Craig D Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - David M Lambert
- Griffith School of Environment and the School of Biomolecular and Physical Sciences, Griffith University, 170 Kessels Road, Nathan, Qld 4111 Australia
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
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25
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Igic B, Leuschner N, Parker KA, Ismar SMH, Gill BJ, Lovegrove TG, Millar CD, Hauber ME. Size dimorphism and avian-perceived sexual dichromatism in a New Zealand endemic bird, the whitehead Mohoua albicilla. J Morphol 2010; 271:697-704. [PMID: 20058295 DOI: 10.1002/jmor.10827] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Sex differences in behavior, morphology, and physiology are common in animals. In many bird species, differences in the feather colors of the sexes are apparent when judged by human observers and using physical measures of plumage reflectance, cryptic (to human) plumage dichromatism has also been detected in several additional avian lineages. However, it remains to be confirmed in almost all species whether sexual dichromatism is perceivable by individuals of the studied species. This latter step is essential because it allows the evaluation of alternative hypotheses regarding the signaling and communication functions of plumage variation. We applied perceptual modeling of the avian visual system for the first time to an endemic New Zealand bird to provide evidence of subtle but consistent sexual dichromatism in the whitehead, Mohoua albicilla. Molecular sexing techniques were also used in this species to confirm the extent of the sexual size dimorphism in plumage and body mass. Despite the small sample sizes, we now validate previous reports based on human perception that in male whiteheads head and chest feathers are physically brighter than in females. We further suggest that the extent of sexual plumage dichromatism is pronounced and can be perceived by these birds. In contrast, although sexual dimorphism was also detectable in the mass among the DNA-sexed individuals, it was found to be less extensive than previously thought. Sexual size dimorphism and intraspecifically perceivable plumage dichromatism represent reliable traits that differ between female and male whiteheads. These traits, in turn, may contribute to honest communication displays within the complex social recognition systems of communally breeding whitehead and other group-breeding taxa.
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Affiliation(s)
- Branislav Igic
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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26
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Abstract
The integrity of extracted ribonucleic acid (RNA) is commonly assessed by gel electrophoresis and subsequent analysis of the ribosomal RNA (rRNA) bands. Using the honey bee, Apis mellifera (Hymenoptera: Apidae), as an example, the electrophoretic rRNA profile of insects is explained. This profile differs significantly from the standard benchmark since the 28S rRNA of most insects contains an endogenous "hidden break." Upon denaturation, the masking hydrogen bonds are disrupted, releasing two similar sized fragments that both migrate closely with 18S rRNA. The resulting rRNA profile thus reflects the endogenous composition of insect rRNA and should not be misinterpreted as degradation.
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Affiliation(s)
- Eva C. Winnebeck
- Department of Anaesthesiology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
- School of Biological Sciences, Faculty of Science The University of Auckland, Auckland, New Zealand
| | - Craig D. Millar
- Department of Anaesthesiology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Guy R. Warman
- Department of Anaesthesiology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
- School of Biological Sciences, Faculty of Science The University of Auckland, Auckland, New Zealand
- , Corresponding author
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27
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Lambert DM, Shepherd LD, Huynen L, Beans-Picón G, Walter GH, Millar CD. The molecular ecology of the extinct New Zealand Huia. PLoS One 2009; 4:e8019. [PMID: 19946368 PMCID: PMC2777306 DOI: 10.1371/journal.pone.0008019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Accepted: 10/19/2009] [Indexed: 11/29/2022] Open
Abstract
The extinct Huia (Heteralocha acutirostris) of New Zealand represents the most extreme example of beak dimorphism known in birds. We used a combination of nuclear genotyping methods, molecular sexing, and morphometric analyses of museum specimens collected in the late 19(th) and early 20(th) centuries to quantify the sexual dimorphism and population structure of this extraordinary species. We report that the classical description of Huia as having distinctive sex-linked morphologies is not universally correct. Four Huia, sexed as females had short beaks and, on this basis, were indistinguishable from males. Hence, we suggest it is likely that Huia males and females were indistinguishable as juveniles and that the well-known beak dimorphism is the result of differential beak growth rates in males and females. Furthermore, we tested the prediction that the social organisation and limited powers of flight of Huia resulted in high levels of population genetic structure. Using a suite of microsatellite DNA loci, we report high levels of genetic diversity in Huia, and we detected no significant population genetic structure. In addition, using mitochondrial hypervariable region sequences, and likely mutation rates and generation times, we estimated that the census population size of Huia was moderately high. We conclude that the social organization and limited powers of flight did not result in a highly structured population.
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Affiliation(s)
- David M Lambert
- Griffith School of Environment and School of Biomolecular and Physical Sciences, Griffith University, Nathan, Australia.
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Subramanian S, Denver DR, Millar CD, Heupink T, Aschrafi A, Emslie SD, Baroni C, Lambert DM. High mitogenomic evolutionary rates and time dependency. Trends Genet 2009; 25:482-6. [PMID: 19836098 DOI: 10.1016/j.tig.2009.09.005] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Revised: 09/11/2009] [Accepted: 09/14/2009] [Indexed: 12/18/2022]
Abstract
Using entire modern and ancient mitochondrial genomes of Adélie penguins (Pygoscelis adeliae) that are up to 44000 years old, we show that the rates of evolution of the mitochondrial genome are two to six times greater than those estimated from phylogenetic comparisons. Although the rate of evolution at constrained sites, including nonsynonymous positions and RNAs, varies more than twofold with time (between shallow and deep nodes), the rate of evolution at synonymous sites remains the same. The time-independent neutral evolutionary rates reported here would be useful for the study of recent evolutionary events.
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Affiliation(s)
- Sankar Subramanian
- Griffith School of Environment, Griffith University, 170 Kessels Road, Nathan, Qld 4111, Australia
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Millar CD, Dodd A, Anderson J, Gibb GC, Ritchie PA, Baroni C, Woodhams MD, Hendy MD, Lambert DM. Mutation and evolutionary rates in adélie penguins from the antarctic. PLoS Genet 2008; 4:e1000209. [PMID: 18833304 PMCID: PMC2546446 DOI: 10.1371/journal.pgen.1000209] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Accepted: 08/25/2008] [Indexed: 12/15/2022] Open
Abstract
Precise estimations of molecular rates are fundamental to our understanding of the processes of evolution. In principle, mutation and evolutionary rates for neutral regions of the same species are expected to be equal. However, a number of recent studies have shown that mutation rates estimated from pedigree material are much faster than evolutionary rates measured over longer time periods. To resolve this apparent contradiction, we have examined the hypervariable region (HVR I) of the mitochondrial genome using families of Adélie penguins (Pygoscelis adeliae) from the Antarctic. We sequenced 344 bps of the HVR I from penguins comprising 508 families with 915 chicks, together with both their parents. All of the 62 germline heteroplasmies that we detected in mothers were also detected in their offspring, consistent with maternal inheritance. These data give an estimated mutation rate (micro) of 0.55 mutations/site/Myrs (HPD 95% confidence interval of 0.29-0.88 mutations/site/Myrs) after accounting for the persistence of these heteroplasmies and the sensitivity of current detection methods. In comparison, the rate of evolution (k) of the same HVR I region, determined using DNA sequences from 162 known age sub-fossil bones spanning a 37,000-year period, was 0.86 substitutions/site/Myrs (HPD 95% confidence interval of 0.53 and 1.17). Importantly, the latter rate is not statistically different from our estimate of the mutation rate. These results are in contrast to the view that molecular rates are time dependent.
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Affiliation(s)
- Craig D. Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Andrew Dodd
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
| | - Jennifer Anderson
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
| | - Gillian C. Gibb
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
| | - Peter A. Ritchie
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
| | - Carlo Baroni
- Dipartmento Scienze della Terra, Università di Pisa, Pisa, Italy
- Consiglio Nazionale Ricerche, Centro Studio Geologia Strutturale, Pisa, Italy
| | - Michael D. Woodhams
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Fundamental Sciences, Massey University Palmerston North, Palmerston North, New Zealand
| | - Michael D. Hendy
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Fundamental Sciences, Massey University Palmerston North, Palmerston North, New Zealand
| | - David M. Lambert
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Auckland, New Zealand
- * E-mail:
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Lawrence HA, Taylor GA, Crockett DE, Millar CD, Lambert DM. New genetic approach to detecting individuals of rare and endangered species. Conserv Biol 2008; 22:1267-1276. [PMID: 18717692 DOI: 10.1111/j.1523-1739.2008.01021.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Many rare and endangered species are difficult to locate, observe, and study. Consequently, many individuals, breeding pairs, and even populations of such species could remain undetected. Genetic markers can potentially be used to detect the existence of undiscovered individuals and populations, and we propose a method to do so that requires 3 conditions. First, sampling of the known population(s) of the target species must be comprehensive. Second, the species must display a reasonable level of philopatry and genetic structuring. Third, individuals must be able to be caught outside of breeding locations (e.g., at courtship or feeding areas, in flight), and the level of recapture must be reasonably high. We applied our method to the Chatham Island Taiko (Pterodroma magentae), one of the world's most endangered seabirds. We sequenced the Taiko mitochondrial cytochrome b gene and both copies of a fragment of the duplicated domain I of the control region. Twenty-one haplotypes were revealed, including 4 (19%) not found in birds at known burrows. These results suggest there are more burrow groups yet to be located. The species is a pelagic gadfly petrel that inhabits land only in the breeding season during which it is nocturnal and nests in burrows. Taiko burrows are situated in dense forest in a remote area of Chatham Island, and are consequently difficult to locate and study. It is important that all Taiko burrows be discovered to enable monitoring and protection of the birds from exotic predators.
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Affiliation(s)
- Hayley A Lawrence
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Albany, Private Bag 102904, NSMC, Auckland, New Zealand
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Millar CD, Huynen L, Subramanian S, Mohandesan E, Lambert DM. New developments in ancient genomics. Trends Ecol Evol 2008; 23:386-93. [PMID: 18501471 DOI: 10.1016/j.tree.2008.04.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Revised: 03/27/2008] [Accepted: 04/04/2008] [Indexed: 11/29/2022]
Abstract
Ancient DNA research is on the crest of a 'third wave' of progress due to the introduction of a new generation of DNA sequencing technologies. Here we review the advantages and disadvantages of the four new DNA sequencers that are becoming available to researchers. These machines now allow the recovery of orders of magnitude more DNA sequence data, albeit as short sequence reads. Hence, the potential reassembly of complete ancient genomes seems imminent, and when used to screen libraries of ancient sequences, these methods are cost effective. This new wealth of data is also likely to herald investigations into the functional properties of extinct genes and gene complexes and will improve our understanding of the biological basis of extinct phenotypes.
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Affiliation(s)
- Craig D Millar
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
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Lawrence HA, Taylor GA, Millar CD, Lambert DM. High mitochondrial and nuclear genetic diversity in one of the world’s most endangered seabirds, the Chatham Island Taiko (Pterodroma magentae). CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9471-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Daniel C, Millar CD, Ismar SMH, Stephenson BM, Hauber ME. Evaluating molecular and behavioural sexing methods for the Australasian gannet (Morus serrator). AUST J ZOOL 2007. [DOI: 10.1071/zo07073] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The availability of molecular methods for avian sex identification has revolutionised the study of sexual differences in behaviour, morphology, life-history traits and conservation management. We implemented the recommendations of a recent review of DNA-based sex-identification by (1) verifying the sex-specificity and (2) estimating the accuracy of different sex-assignment methods in an apparently monomorphic seabird, the Australasian gannet (Morus serrator). The polymerase chain reaction (PCR) method based on the amplification of the sex-linked chromodomain-helicase-DNA binding gene (CHD) repeatedly assigned the same sex in 96% (n = 27 replicates) and correctly sexed all individuals with known gonadal anatomy (n = 6). PCR and sex-specific restriction fragment length polymorphism (RFLPs) showed agreement for 99.5% of individuals (n = 201). DNA-sexed pairs known to be social mates consisted of a male and a female in 96% of pairs sexed by PCR (n = 77) and 98% of pairs sexed by RFLP (n = 65). DNA-sexed females were in the bottom and males in the top copulatory position in 86% of observed copulations (n = 43 individuals). These results validate assumptions that both membership in social pairs and different copulatory positions can serve as reliable behavioural proxies for field-based sex identification in this colonial and obligately biparental seabird.
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Shepherd LD, Millar CD, Ballard G, Ainley DG, Wilson PR, Haynes GD, Baroni C, Lambert DM. Microevolution and mega-icebergs in the Antarctic. Proc Natl Acad Sci U S A 2005; 102:16717-22. [PMID: 16275908 PMCID: PMC1283793 DOI: 10.1073/pnas.0502281102] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2005] [Indexed: 11/18/2022] Open
Abstract
Microevolution is regarded as changes in the frequencies of genes in populations over time. Ancient DNA technology now provides an opportunity to demonstrate evolution over a geological time frame and to possibly identify the causal factors in any such evolutionary event. Using nine nuclear microsatellite DNA loci, we genotyped an ancient population of Adélie penguins (Pygoscelis adeliae) aged approximately 6,000 years B.P. Subfossil bones from this population were excavated by using an accurate stratigraphic method that allowed the identification of individuals even within the same layer. We compared the allele frequencies in the ancient population with those recorded from the modern population at the same site in Antarctica. We report significant changes in the frequencies of alleles between these two time points, hence demonstrating microevolutionary change. This study demonstrates a nuclear gene-frequency change over such a geological time frame. We discuss the possible causes of such a change, including the role of mutation, genetic drift, and the effects of gene mixing among different penguin populations. The latter is likely to be precipitated by mega-icebergs that act to promote migration among penguin colonies that typically show strong natal return.
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Affiliation(s)
- L D Shepherd
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Albany, Auckland, New Zealand
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Baker AJ, Huynen LJ, Haddrath O, Millar CD, Lambert DM. Reconstructing the tempo and mode of evolution in an extinct clade of birds with ancient DNA: the giant moas of New Zealand. Proc Natl Acad Sci U S A 2005; 102:8257-62. [PMID: 15928096 PMCID: PMC1149408 DOI: 10.1073/pnas.0409435102] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2004] [Accepted: 04/04/2005] [Indexed: 11/18/2022] Open
Abstract
The tempo and mode of evolution of the extinct giant moas of New Zealand remain obscure because the number of lineages and their divergence times cannot be estimated reliably by using fossil bone characters only. We therefore extracted ancient DNA from 125 specimens and genetically typed them for a 658-bp mtDNA control region sequence. The sequences detected 14 monophyletic lineages, 9 of which correspond to currently recognized species. One of the newly detected lineages was a genetically divergent form of Megalapteryx originally described as a separate species, two more were lineages of Pachyornis in southern and northeastern New Zealand, and two were basal lineages of South Island Dinornis. When results from genetic typing and previous molecular sexing were combined, at least 33.6% of the specimens were incorrectly classified. We used longer sequences of the control region and nine other mtDNA genes totaling 2,814 base pairs to derive a strongly supported phylogeny of the 14 moa lineages. Molecular dating estimated the most recent common ancestor of moas existed after the Oligocene drowning of New Zealand. However, a cycle of lineage-splitting occurred approximately 4-10 million years ago, when the landmass was fragmented by tectonic and mountain-building events and general cooling of the climate. These events resulted in the geographic isolation of lineages and ecological specialization. The spectacular radiation of moa lineages involved significant changes in body size, shape, and mass and provides another example of the general influence of large-scale paleoenvironmental changes on vertebrate evolutionary history.
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Affiliation(s)
- Allan J Baker
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON, Canada M5S 2C6.
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Abstract
A complete DNA-based inventory of the Earth's present biota using large-scale high-throughput DNA sequencing of signature region(s) (DNA barcoding) is an ambitious proposal rivaling the Human Genome Project. We examine whether this approach will also enable us to assess the past diversity of the earth's biota. To test this, we sequenced the 5' terminus of the mitochondrial cytochrome c oxidase I (COI) gene of individuals belonging to a group of extinct ratite birds, the moa of New Zealand. Moa comprised a large number of taxa that radiated in isolation on this oceanic landmass. Using a phylogenetic approach based on a large data set including protein coding and 12S DNA sequences as well as morphology, we now have precise information about the number of moa species that once existed. We show that each of the moa species detected using this extensive data set has a unique COI barcode(s) and that they all show low levels of within-species COI variation. Consequently, we conclude that COI sequences accurately identify the species discovered using the larger data set. Hence, more generally, this study suggests that DNA barcoding might also help us detect other extinct animal species and that a large-scale inventory of ancient life is possible.
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Affiliation(s)
- D M Lambert
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Private Bag 102 904, Auckland, New Zealand.
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Ritchie PA, Millar CD, Gibb GC, Baroni C, Lambert DM. Ancient DNA enables timing of the pleistocene origin and holocene expansion of two adélie penguin lineages in antarctica. Mol Biol Evol 2003; 21:240-8. [PMID: 14595092 DOI: 10.1093/molbev/msh012] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The timing of divergent events in history is one of the central goals of contemporary evolutionary biology. Such studies are however dependent on accurate evolutionary rates. Recent developments in ancient DNA analysis enable the estimation of more accurate evolutionary rates and therefore more accurate timing of divergence events. Consequently, this leads to a better understanding of changes in populations through time. We use an evolutionary rate calculated from ancient DNA of Adélie penguins (Pygoscelis adeliae) to time divergent events in their history. We report the presence of two distinct and highly variable mitochondrial DNA lineages and track changes in these lineages through space and time. When the ancient DNA and the phylogenetic rates are used to estimate the time of origin of the lineages, two very different estimates resulted. In addition, these same rates provide very different estimates of the time of expansion of these lineages. We suggest that the rate calculated from ancient DNA is more consistent with the glacial history of Antarctica and requires fewer assumptions than does a narrative based on the phylogenetic rate. Finally, we suggest that our study indicates an important new role for ancient DNA studies in the timing of divergent events in history.
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Affiliation(s)
- Peter A Ritchie
- Allan Wilson Centre for Molecular Ecology and Evolution, Auckland
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Huynen L, Millar CD, Scofield RP, Lambert DM. Nuclear DNA sequences detect species limits in ancient moa. Nature 2003; 425:175-8. [PMID: 12968179 DOI: 10.1038/nature01838] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2003] [Accepted: 06/03/2003] [Indexed: 11/09/2022]
Abstract
Ancient DNA studies have typically used multi-copy mitochondrial DNA sequences. This is largely because single-locus nuclear genes have been difficult to recover from sub-fossil material, restricting the scope of ancient DNA research. Here, we have isolated single-locus nuclear DNA markers to assign the sex of 115 extinct moa and, in combination with a mitochondrial DNA phylogeny, tested competing hypotheses about the specific status of moa taxa. Moa were large ratite birds that showed extreme size variation both within and among species. For some taxa, this large variation was hypothesized to represent sexual dimorphism, while for others it was argued to reflect the existence of different species. Our results show that moa were characterized by extreme reverse sexual dimorphism and as a result we have been able to clarify the number of moa species. For example, we show that the three recognized 'species' of Dinornis comprised only two monophyletic groups and that two of these 'species' comprised individuals of one sex only. This study also illustrates that single-locus nuclear DNA sequences can be consistently recovered from ancient material.
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Affiliation(s)
- L Huynen
- Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Molecular BioSciences, Massey University, Private Bag 102 904, Auckland, New Zealand
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Abstract
DNA-based sex tests now exist for many avian species. However, none of these tests are widely applicable to ratites. We present DNA sequence data for a locus that is W chromosome-linked in the kiwi, ostrich, cassowary, rhea, and emu. At the amino acid level, this sequence has significant homology to X-linked genes in platyfish and Caenorhabditis elegans. Polymerase chain reaction (PCR) primers designed to this locus allow the assignment of sex in all species of living ratites.
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Affiliation(s)
- Leon Huynen
- Institute of Molecular BioSciences and Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Private Bag 11-222, Palmerston North, New Zealand
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Abstract
Well-preserved subfossil bones of Adélie penguins, Pygoscelis adeliae, underlie existing and abandoned nesting colonies in Antarctica. These bones, dating back to more than 7000 years before the present, harbor some of the best-preserved ancient DNA yet discovered. From 96 radiocarbon-aged bones, we report large numbers of mitochondrial haplotypes, some of which appear to be extinct, given the 380 living birds sampled. We demonstrate DNA sequence evolution through time and estimate the rate of evolution of the hypervariable region I using a Markov chain Monte Carlo integration and a least-squares regression analysis. Our calculated rates of evolution are approximately two to seven times higher than previous indirect phylogenetic estimates.
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Affiliation(s)
- D M Lambert
- Institute of Molecular BioSciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand.
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Millar CD, Taylor GA, Moore PJ, Halverson JL, Lambert DM. A novel restriction fragment length polymorphism for petrels or tube-nosed seabirds. Mol Ecol 2000; 9:1915-7. [PMID: 11091328 DOI: 10.1046/j.1365-294x.2000.01061.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- C D Millar
- Institute of Molecular BioSciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand.
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Lambert DM, Millar CD, Hughes TJ. On the classic case of natural selection. Riv Biol 1999; 92:499-501. [PMID: 10765683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- D M Lambert
- Department of Zoology, University of Auckland, New Zealand
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Abstract
A central biological parameter in the study of any animal population is the accurate assignment of sex. Indeed any ecological study of a population requires information on sex composition in relation to such biological factors as behaviour, movement, mortality and birth rate. However, our ability to assign the sex of adults of many avian species is poor and the sexing of young is universally difficult. We report here the successful application of a molecular technique for the assignment of sex in the communally breeding pukeko or purple swamphen (Porphyrio porphyrio melanotus). W- and Z-linked chromosome fragments in digested genomic DNA of pukeko were detected with the DNA probe pMg1. We consequently show that this species breeds in polyandrous, polygynous and polygynandrous groups. Finally we discuss why recent molecular methods represent important new tools in ecology.
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Affiliation(s)
- C D Millar
- Centre for Conservation Biology, School of Biological Sciences, University of Auckland, New Zealand
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Abstract
A wide array of DNA-based genetic techniques are now available for the study of many problems in conservation biology. Either directly or indirectly, such techniques are becoming increasingly available to scientists and managers alike. Although these technologies are generally known to conservationists, there is a need to clearly outline the principal characteristics of such genetic tools and to detail how they can most appropriately be used in the management of wildlife species. The essential characteristics of mitochondrial and chloroplast restriction fragment analyses are detailed, together with discussions of single locus nuclear restriction fragment length polymorphisms (RFLPs), multilocus DNA fingerprinting, microsatellite DNA, randomly amplified polymorphic DNAs (RAPDs), and DNA sequence variation. We also give relevant information about the development times for these techniques, their relative costs, and the quality of tissue required. In addition, we discuss which conservation problems are appropriate to each of these methods and give examples of their application and potential use in relation to New Zealand organisms. The following problems are considered: sex assignment; parentage and kinship; migration; species, population and strain identification; forensic applications; genetic effects of population bottlenecks; disease identification; feeding preferences; philopatry; pest control; and understanding population extinction. Finally, we suggest that both microsatellite and minisatellite DNA techniques have particular advantages over many other currently-available techniques and conclude that these two approaches are applicable to a wide range of the conservation problems.
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Lambert DM, Millar CD, Jack K, Anderson S, Craig JL. Single- and multilocus DNA fingerprinting of communally breeding pukeko: do copulations or dominance ensure reproductive success? Proc Natl Acad Sci U S A 1994; 91:9641-5. [PMID: 7937821 PMCID: PMC44869 DOI: 10.1073/pnas.91.20.9641] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
In behavioral and ecological studies the "function" of dominance hierarchies is thought to be related to reproductive success. In particular, dominant males are regarded as likely to gain a reproductive advantage due to enhanced "access" to females. We compare the dominance status of adults with the frequency of copulations and the patterns of parentage in communally breeding pukeko or purple swamphen (Porphyrio porphyrio melanotus). This avian species has an unusual social system, often breeding in polygynandrous groups in which there is a strong dominance hierarchy. Typically, during the breeding season, there is considerable sexual activity, with heterosexual and homosexual copulations between adults being commonplace. Hae III-digested DNA from individuals belonging to breeding groups was hybridized to the minisatellite DNA probe YNH24, revealing putative single-locus profiles, while hybridization of the same DNA to the minisatellite probes pV47-2, 3'HVR, and per revealed typical multilocus profiles. The numbers of unattributable restriction fragments allowed the maternity and paternity of all individuals to be conclusively determined, despite high levels of band sharing among individuals within breeding groups. These close genetic similarities are a likely consequence of strong philopatry and inbreeding. We report instances of males which are high on the dominance hierarchy but have only a limited reproductive output in comparison with others and males which are subordinate but achieve a significant proportion of fertilizations. Generally these data reveal no consistent relationship between dominance, the frequency of copulations, and parentage among males. We conclude that pukeko highlight some difficulties with conventional explanations for the "function" of dominance.
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Affiliation(s)
- D M Lambert
- School of Biological Sciences, University of Auckland, New Zealand
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