The mysterious Spotted Green Pigeon and its relation to the Dodo and its kindred

Heupink, Tim H.; Grouw, Hein van; Lambert, David M.

doi:10.1186/1471-2148-14-136

Cited by 15 publications

(9 citation statements)

References 14 publications

(16 reference statements)

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“…A more recent analysis using mitochondrial 12S sequences show similar relationships: Raphinae as the sister taxon to Ca. nicobarica , followed by a clade composed of D. strigirostris and the Goura clade (Heupink et al ., ; Fig. D).…”

Section: Introductionmentioning

confidence: 83%

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The first endocast of the extinct dodo (Raphus cucullatus) and an anatomical comparison amongst close relatives (Aves, Columbiformes)

2016

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The dodo (Raphus cucullatus) became extinct only 100 years after humans first arrived on the Indian Ocean island of Mauritius. Even though it has become an example of oddity, obsolescence, stupidity, and extinction, most aspects of its biology are still unknown. We used high-resolution X-ray computed tomography (CT) scanning to examine the endocranial morphology of the dodo and compare this virtual endocast to eight close relatives. Enlarged olfactory bulbs are a shared characteristic of the Raphinae and posteriorly angled semicircular canals are particular to the dodo compared with the other eight species sampled here. A regression of log endocranial volume against log body size shows that the dodo has an endocranial volume on par with other pigeons. Aspects of the dodo's biology are discussed in relation to these endocranial features.

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Section: Introductionmentioning

confidence: 83%

“…D, the Raphinae are sister to Caloenas . Redrawn from Heupink et al ., ;. E, the Raphinae are sister to Caloenas .…”

Section: Introductionmentioning

confidence: 99%

The first endocast of the extinct dodo (Raphus cucullatus) and an anatomical comparison amongst close relatives (Aves, Columbiformes)

2016

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“…The advent of the polymerase chain reaction (PCR) technique, nearly 30 years ago, was key in enabling researchers to obtain genetic data from museum samples and to produce more thorough genetic or phylogenetic hypotheses by increasing population or taxon sampling, sometimes using specimens of long-extinct species (e.g. Shapiro et al, 2002;Warren et al, 2006;Johnson et al, 2010;Shepherd et al, 2012;Heupink, van Grouw & Lambert, 2014). Museum specimens have therefore contributed to the description of many specific evolutionary and biogeographic patterns, such as, for example, the recent intercontinental spread of cultivated plants (Ames & Spooner, 2008;Schaefer & Renner, 2010), the evolution of extant and extinct ruminants (Decker et al, 2009), or the origin of the dodo (Shapiro et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

Valuing museum specimens: high-throughput DNA sequencing on historical collections of New Guinea crowned pigeons (Goura)

Besnard

Bertrand

Delahaie

et al. 2015

Biol. J. Linn. Soc.

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Museum specimens are of particular importance for investigating systematics and the biogeography as well as other aspects of the evolution of biodiversity. They are also a depository of specimens accumulated over recent historical times and often the only way to study recently extinct or rare species. Unfortunately, most museum specimens yield low-quality DNA limiting their generalized use in phylogenetic and population genetic studies. Advances in sequencing technologies now offer opportunities to analyse such material even from very small tissue. Here, we applied the Illumina technology (HiSeq) on three specimens of crowned pigeon (Goura spp.) collected in New Guinea between 1879 and 1934. A shotgun strategy allowed us to quickly and reliably assemble complete mitochondrial genomes and fragments of three single-copy gene phylogenetic markers even with low double-stranded DNA quantity (9 to 69 ng). Phylogenetic assignments of these new sequences confirmed them as Goura sequences. Therefore, our study confirms the power of using next-generation sequencing methods to investigate the evolutionary history of species for which access to fresh samples is limited but museum collections are available. These approaches are considerably increasing the value of many natural history collections for genetic investigations, particularly from biodiversity hotspots that are presently difficult to prospect.

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“…The fact that we could not replicate the original results by Adcock et al (3) is perhaps not surprising given that they were obtained by PCR-based methods applied to samples recovered from Holocene and Pleistocene deposits in semiarid and temperate Australia. The methods used here present advantages over PCR, in that they are able to target very degraded templates and improve the ability to distinguish authentic sequences from contaminants (19,28,29,33,34). These approaches have allowed us to clarify the results for the four Willandra Lakes individuals analyzed by Adcock et al (3); only WLH3 (Mungo Man) and WLH4 contained verifiable human DNA, whereas nothing could be retrieved from extracts of WLH15 and WLH55.…”

Section: Resultsmentioning

confidence: 97%

Ancient mtDNA sequences from the First Australians revisited

Heupink

Subramanian

Wright

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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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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The mysterious Spotted Green Pigeon and its relation to the Dodo and its kindred

Cited by 15 publications

References 14 publications

The first endocast of the extinct dodo (Raphus cucullatus) and an anatomical comparison amongst close relatives (Aves, Columbiformes)

The first endocast of the extinct dodo (Raphus cucullatus) and an anatomical comparison amongst close relatives (Aves, Columbiformes)

Valuing museum specimens: high-throughput DNA sequencing on historical collections of New Guinea crowned pigeons (Goura)

Ancient mtDNA sequences from the First Australians revisited

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