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Cited by 1Genetic diversity and population structureForensic and Genetic ResearchGenomics and Phylogenetic Studies

Mitogenomic Crocodylia phylogeny and population structure of Crocodylus porosus including the extinct Seychelles crocodile

Open access
Agne, Stefanie, Arnold, Patrick, Belle, Berthilde, Straube, Nicolas, Hofreiter, Michael, Glaw, Frank·2026·Royal Society Open Science
DOI 10.1098/rsos.251546
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Abstract

This study investigates the phylogenetic relationships of extant crocodiles and the population structure of the saltwater crocodile (Crocodylus porosus). We combined mitochondrial genomes from museum specimens with genetic data from modern samples to reconstruct the evolutionary history of the saltwater crocodile and clarify the identity of the extinct Seychelles crocodile. Mitochondrial genomes were sequenced for 11 museum specimens of Crocodylus halli, C. niloticus, C. novaeguineae, C. palustris and C. porosus, including the Seychelles crocodile. In addition, the mitochondrial control and ND4 regions were analysed for 187 and 13 C. porosus individuals, respectively. This study provides the most comprehensive Crocodylus phylogeny to date, establishes the phylogenetic placement of the extinct Seychelles crocodile as a distant population of the saltwater crocodile and provides no mitochondrial support for C. halli as a distinct species from C. novaeguineae. Nineteen haplotypes were identified among C. porosus samples, showing no clear mitochondrial geographic structure. However, this probably reflects the limited resolution of mitochondrial DNA rather than true genetic homogeneity, consistent with nuclear genomic studies revealing strong regional differentiation. Our results highlight the need for conservation strategies that recognize the broad genetic connectivity of C. porosus populations rather than emphasizing subspecies distinctions.

AI snapshot

Written from the paper’s full text.

TL;DR

This study reconstructs mitochondrial genomes from museum specimens, including the extinct Seychelles crocodile, to resolve Crocodylia phylogeny and *Crocodylus porosus* population structure. It places the Seychelles crocodile as the westernmost *C. porosus* population, finds no mitochondrial support for *C. halli* as a distinct species, and reports low mitochondrial differentiation across *C. porosus* despite significant pairwise population differentiation.

Key findings

  • The extinct Seychelles crocodile is nested within *C. porosus* as sister to a clade including samples from Borneo, Buru, Papua New Guinea, Sumatra and India; its Kimura-2-parameter distance to other *C. porosus* sequences is 0.005, versus 0.024 between undisputed species *C. mindorensis* and *C. novaeguineae*.
  • The southern New Guinea *C. halli* specimen is nested with other *C. novaeguineae*; its distance to other *C. novaeguineae* is 0.001, and the paper concludes *C. halli* should be considered a junior synonym of *C. novaeguineae* from a mitochondrial perspective.
  • Among 187 *C. porosus* individuals surveyed for 541 bp of mtDNA control region, 26 polymorphic sites and 19 haplotypes were found; overall haplotype diversity was 0.840, nucleotide diversity 0.0056, and mean nucleotide divergence among populations 0.0032, with no clear mitochondrial geographic structure.
  • Pairwise *F*st values were significantly different from zero for all 11 geographic populations; the highest was 0.88334 between northern Papua New Guinea islands and northeast Papua New Guinea, and the lowest was 0.12617 between northern Papua New Guinea islands and northwest Papua New Guinea. Dating analyses estimated the Crocodylia MRCA at 87.4 Ma (95% HPD 82.4–93.3 Ma) and the *Crocodylus* MRCA at 18.37 Ma (95% HPD 17.0–19.8 Ma).

Methods

  • Mitochondrial genomes were sequenced from 11 museum specimens of *C. porosus* (6), *C. niloticus* (1), *C. palustris* (1) and *C. novaeguineae* (3, including *C. halli*), mostly more than 100 years old, and aligned with 64 additional NCBI mitochondrial genomes.
  • Phylogenetic analyses used MrBayes and RAxML; divergence times were estimated in BEAST under a strict clock with a Crocodylia calibration of 77.8–83.6 Ma.
  • Population analyses used 187 *C. porosus* control-region sequences (541 bp analysed) and ND4 data for 13 individuals; diversity was assessed in DNAsp, pairwise *F*st in Arlequin, and median-joining haplotype networks in PopART.

Limitations

  • The paper states that sampling from the Sunda Shelf, Eastern India and the Seychelles was too limited to test for population differentiation.
  • The paper states that mitochondrial DNA reflects only female-mediated gene flow and may overlook male-driven connectivity; it also notes that limited mitochondrial differentiation may reflect the conservative nature of the crocodilian mitochondrial genome rather than true absence of population structure, consistent with nuclear genomic studies showing regional differentiation.
  • The paper states that the relaxed clock model did not achieve ESS values >200, so only the strict clock results were used. Evident from the text: taxonomic conclusions about *C. halli* and subspecies are based on mitochondrial data alone, and some modern samples came from captive or captive-bred crocodiles.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1098/rsos.251546

Cites

62 of 62 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

11 of 25 cited sources checked · 4 supported · 0 flagged · accuracy not yet measured

  • Interpretationown data

    The analysis of mitochondrial genomes aligns with previously dated phylogenies of Crocodylia.

    “Our analysis of mitochondrial genomes (figure 1) aligns with previously dated phylogenies of Crocodylia [35,48], supporting and consolidating our picture of crocodilian evolution.”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites [35] Pan, 2021, Near-complete phylogeny of extant Crocodylia (Reptilia) using mitogenome-based data, Zool. J. Linn. Soc. source

      The available passages are from the reference list (page unavailable). They name earlier mitogenomic and time-calibrated Crocodylia studies, but do not compare this paper’s results with those phylogenies. Searches for divergence times and agreement with previous studies did not retrieve a passage that establishes the claimed alignment. (LLM, conf=0.72)

      Experimental — accuracy not yet measured
    • cites [48] Hekkala, 2021, Paleogenomics illuminates the evolutionary history of the extinct Holocene ‘horned’ crocodile of Madagascar, Voay robustus, Commun. Biol. source

      The Results (page not provided) say the mitochondrial analyses corroborate previously supported relationships among the nine extant crocodylian genera. But they also say the mitochondrial trees contradict earlier analyses that placed Voay with osteolaemines; the paper does not establish general agreement with previously dated phylogenies. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
  • Findingcitation

    Our estimated node age of 24.54 Ma for the Crocodylus crown group is consistent with the divergence between Voay robustus and Crocodylus at approximately 24.9 Ma reported by Hekkala et al. [48].

    “Our estimated node age of 24.54 Ma for the Crocodylus crown group is consistent with the divergence between Voay robustus and Crocodylus at approximately 24.9 Ma reported by Hekkala et al. [48].”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [48] Hekkala, 2021, Paleogenomics illuminates the evolutionary history of the extinct Holocene ‘horned’ crocodile of Madagascar, Voay robustus, Commun. Biol. source
  • Findingcitation

    Nucleotide diversity in northeast Papua New Guinea and all the northern Papua New Guinea Island sub-populations was minimal.

    “Additionally, nucleotide diversity in northeast Papua New Guinea and all the northern Papua New Guinea Island sub-populations was minimal, as expected for relatively recently colonized populations [67].”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [67] Whitlock, 1990, Some population genetic consequences of colony formation and extinction: genetic correlations within founding groups, Evolution source

      The Genetic Variation Among section (page unavailable) models how founding-group size affects within-population allele identity, providing a conditional rationale for lower diversity after colonization. It does not report nucleotide diversity in northeast Papua New Guinea or the northern island sub-populations, nor establish that their diversity was minimal. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
  • Findingown data

    Nineteen haplotypes were identified among C. porosus samples.

    “Nineteen haplotypes were identified among C. porosus samples”
    • Also stated in: § 3.2. Genetic diversity among populations from C. porosus · plain
      “a total of 19 haplotypes”
    Quote in the paperNot a substantial claim
  • Findingown data

    No deep phylogeographic clustering is recognisable among C. porosus control region haplotypes.

    “No deep phylogeographic clustering is recognisable.”
    Quote in the paperSubstantial claim
  • May combine two claims. 24
  • Classified as probably not a substantial claim. 5

  • May combine two claims.

    Premisecitation

    Recent studies employing genome-wide SNP data have demonstrated substantial phylogeographic structure within C. porosus in Australia, indicating restricted gene flow and regional adaptation.

    “Recent studies employing genome-wide SNP data [68][69][70] have demonstrated substantial phylogeographic structure within C. porosus in Australia, indicating restricted gene flow and regional adaptation.”
    Quote in the paperSubstantial claim3 of 3 sources checked
    • cites [68] Fukuda, 2022, Environmental resistance and habitat quality influence dispersal of the saltwater crocodile, Mol. Ecol. source

      The Results, ‘Genetic diversity and population structure’ (page unavailable), report SNP-based differentiation and isolation by distance among northern Australian crocodiles, consistent with geographically limited gene flow. But individuals clustered only loosely by location, so ‘substantial phylogeographic structure’ overstates the finding; the cited paper does not establish regional adaptation. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
    • cites [69] Fukuda, 2019, Translocation, genetic structure and homing ability confirm geographic barriers disrupt saltwater crocodile movement and dispersal, PLoS One source

      The Results (Genetic analysis; page not provided) report regional clustering in 8,312 SNPs and less gene flow across the Cobourg Peninsula than among neighbouring populations on the same side. This supports geographic genetic structure and restricted gene flow in the sampled Northern Territory crocodiles, but the paper does not demonstrate regional adaptation. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites [70] Lloyd-Jones, 2023, Implications of past and present genetic connectivity for management of the saltwater crocodile (Crocodylus porosus), Evol. Appl. source

      The Results report genome-wide SNP data from Queensland crocodiles, and the Discussion (‘Limited dispersal and site fidelity’; page unavailable) reports substantial geographic genetic differentiation and historically constrained genetic exchange. The cited paper therefore supports the structure and restricted-gene-flow portions of the claim, but the passages do not establish regional adaptation. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The geographical range of C. porosus encompasses a well-known phylogeographic boundary, the Indo-Pacific Barrier, that affects many Indo-Pacific species.

    “The geographical range of C. porosus encompasses a well-known phylogeographic boundary, the Indo-Pacific Barrier, that affects many Indo-Pacific species (e.g., gastropods [56]; reef fish [57]).”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [56] Crandall, 2008, Contrasting demographic history and phylogeographical patterns in two Indo-Pacific gastropods, Mol. Ecol. source
    • cites [57] Gaither, 2011, Phylogeography of the reef fish Cephalopholis argus (Epinephelidae) indicates Pleistocene isolation across the indo-pacific barrier with contemporary overlap in the coral triangle, BMC Evol. Biol. source

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductown data

    Convergence between BEAST runs was checked using Tracer v. 1.7, ensuring that ESS values were >200 to indicate adequate sampling.

    “We checked for convergence between runs using Tracer v. 1.7 [36], ensuring that ESS values were >200 to indicate adequate sampling.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [36] Rambaut, 2018, Posterior summarization in Bayesian phylogenetics using tracer 1.7, Syst. Biol. source

  • May combine two claims.

    Interpretationreasoning

    This consistency between molecular clock estimates reinforces the hypothesis that Voay represents a sister lineage to the crown Crocodylus, diverging around the Oligocene-Miocene boundary.

    “This consistency between molecular clock estimates reinforces the hypothesis that Voay represents a sister lineage to the crown Crocodylus, diverging around the Oligocene-Miocene boundary.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [48] Hekkala, 2021, Paleogenomics illuminates the evolutionary history of the extinct Holocene ‘horned’ crocodile of Madagascar, Voay robustus, Commun. Biol. source

  • May combine two claims.

    Interpretationcitation

    These adaptations facilitate an ability to disperse across marine barriers, as shown by cases of sea crossings from the nearest breeding population over hundreds of kilometres with probably daily movements of over 20 km.

    “These adaptations clearly facilitate an ability to disperse across marine barriers, shown by cases in which dispersal involved sea crossings from the nearest breeding population over hundreds of kilometres with probably daily movements of over 20 km [65].”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [65] Read, 2007, Satellite tracking reveals long distance coastal travel and homing by translocated Estuarine Crocodiles, Crocodylus porosus, PLoS One source

      The Discussion (page unavailable) reports that one translocated crocodile travelled more than 20 km per day for 20 days and links sustained exercise and salt glands to long-distance dispersal. The Results and Abstract (pages unavailable) describe a coastal homing journey of more than 400 km, not a documented sea crossing from the nearest breeding population. That specific example of dispersal across a marine barrier is not supported by this paper. (LLM, conf=0.87)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Findingown data

    Two samples from Australia show a higher degree of divergence in the ND4 region, with nine mutational steps separating them from the other populations.

    “However, two samples from Australia show a higher degree of divergence, with nine mutational steps separating them from the other populations.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Within-population estimates of haplotype and nucleotide diversity in C. porosus were low and differed greatly between populations.

    “Within population estimates of haplotype and nucleotide diversity were also low and differed greatly between populations.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Overall haplotypic diversity in C. porosus was relatively high (0.840), whereas nucleotide diversity (0.0056) and mean nucleotide divergence among populations (0.0032) were low.

    “Overall haplotypic diversity was relatively high (0.840), whereas nucleotide diversity (0.0056) and mean nucleotide divergence among populations (0.0032) were low”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Fst values were significantly different from zero for all pairwise combinations, representing significant amounts of genetic differentiation among the 11 geographic populations investigated.

    “F st values were significantly different from zero for all pairwise combinations, representing significant amounts of genetic differentiation among the 11 geographic populations investigated”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The relationships in the Crocodylus tree are mostly well-supported, with posterior probabilities >0.95 and bootstrap support values >95.

    “The relationships in the tree are mostly well-supported, i.e. posterior probabilities >0.95 and bootstrap support values >95.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The haplotype network reveals three haplotypes in Australia, with several mutational steps between them.

    “The haplotype network (figure 2) reveals three haplotypes in Australia, with several mutational steps between them.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationcitation

    The limited mitogenetic diversity of C. porosus, despite its deep intraspecific coalescence of over 2 million years, confirms the low mitochondrial substitution rates in crocodiles.

    “The limited mitogenetic diversity of C. porosus, despite its deep intraspecific coalescence of over 2 million years (figure 1; table 2), confirms the low mitochondrial substitution rates in crocodiles (as also shown for C. moreletii [52]).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [52] Ray, 2004, Low levels of nucleotide diversity in Crocodylus moreletii and evidence of hybridization with C. acutus, Conserv. Genet. source

  • May combine two claims.

    Interpretationnone given

    Until the extinction of the Seychelles population, the range of C. porosus spanned over 12,000 km west-east from Vanuatu in the Pacific Ocean to the Seychelles in the western Indian Ocean, and over 5000 km north-south.

    “Until the extinction of the Seychelles population, the range of C. porosus spanned over 12 000 km in west-east direction from Vanuatu in the Pacific Ocean to the Seychelles in the western Indian Ocean, and over 5000 km in north-south direction.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    The small mitochondrial distances among C. porosus populations throughout its vast distribution range and the presence of three different haplotypes in Australia do not support the recognition of any subspecies within C. porosus (C. p. australis, C. p. minikanna, C. p. biporcatus).

    “The small mitochondrial distances among C. porosus populations throughout its vast distribution range and the presence of three different haplotypes in Australia do not support the recognition of any subspecies within C. porosus (C.p. australis, C. p. minikanna, C. p. biporcatus), which were suggested by some authors [53][54][55].”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [53] Deraniyagala, 1953

      Not checked in the free run.

    • cites [54] Deraniyagala, 1955, A new race of estuarine crocodile from Ceylon, Spolia Zeylan

      Not checked in the free run.

    • cites [55] Wermuth, 1977

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    The extinct Seychelles crocodile was a population of C. porosus (the saltwater crocodile), specifically its westernmost population, rather than an endemic Seychelles species or a population of C. niloticus or C. palustris.

    “establishes the phylogenetic placement of the extinct Seychelles crocodile as a distant population of the saltwater crocodile”
    • Also stated in: § 4.1. Phylogenetic placement of the Seychelles crocodile and Crocodylus systematics · boosted
      “It also demonstrates that the extinct Seychelles crocodile was actually the westernmost population of C. porosus, as suggested by Gerlach & Canning [4] based on their morphological identification, rather than being an endemic species of the Seychelles or a population of C. niloticus or C. palustris”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    The three mitochondrial haplotypes identified in Australian C. porosus populations also occur in other parts of the species' range, indicating historical maternal gene flow across regional populations.

    “The three mitochondrial haplotypes identified in Australian C. porosus populations also occur in other parts of the species' range, indicating historical maternal gene flow across regional populations.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    Long-distance movements by saltwater crocodiles may not be rare and marine barriers probably do not pose a significant obstruction to movement in this species.

    “These records suggest that long-distance movements by saltwater crocodiles may not be rare and that marine barriers probably do not pose a significant obstruction to movement in this species.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Our data call for a simplification of Crocodylus taxonomy on both the species and subspecies levels and a synonymization of several taxa.

    “In summary, our data call for a simplification of Crocodylus taxonomy on both the species and subspecies levels and a synonymization of several taxa.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    On the Sunda Shelf, freshwater connections probably occurred between various regions, including Southeast Asia, eastern Peninsula Malaysia, and parts of Borneo and Sumatra, although a central ridge in the Java Sea separated some areas.

    “On the Sunda Shelf, freshwater connections probably occurred between various regions, including Southeast Asia, eastern Peninsula Malaysia, and parts of Borneo and Sumatra, although a central ridge in the Java Sea separated some areas [58,59].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [58] Voris, 2000, Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations, J. Biogeogr. source
    • cites [59] De Bruyn, 2004, Reconciling geography and genealogy: phylogeography of giant freshwater prawns from the Lake Carpentaria region, Mol. Ecol. source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    High ESS values (>200) were found for all parameters in the BEAST analysis under a strict clock model used to estimate the divergence time of the different Crocodylia species.

    “High ESS values (>200) were found for all parameters in the BEAST analysis under a strict clock model used to estimate the divergence time of the different Crocodylia species (figure 1).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    A minimum depth of 3 was ensured by remapping the reads of the last iteration to corresponding references again using BWA.

    “A minimum depth of 3 was ensured by remapping the reads of the last iteration to corresponding references again using BWA”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    At the height of the last glacial maximum, the Indo-Pacific Sea level dropped about 120 m, exposing the Sunda and Sahul shelves and isolating marine and coastal faunas of the Indian and Pacific Ocean.

    “At the height of the last glacial maximum, the Indo-Pacific Sea level dropped about 120 m, exposing the Sunda and Sahul shelves and isolating marine and coastal faunas of the Indian and Pacific Ocean [58,60].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [58] Voris, 2000, Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations, J. Biogeogr. source
    • cites [60] Bintanja, 2005, Modelled atmospheric temperatures and global sea levels over the past million years, Nature source

  • May combine two claims.

    Interpretationown data

    The extinct Seychelles crocodile was the westernmost population of C. porosus, not an endemic species or a population of C. niloticus.

    “It supports existing phylogenies and clarifies that the extinct Seychelles crocodile was the westernmost population of C. porosus, not an endemic species or a population of C. niloticus.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    The Sunda Shelf seems to contain several interconnected endemic haplotypes, suggesting that it may have been a centre of diversification.

    “Interestingly, the Sunda Shelf seems to contain several interconnected endemic haplotypes, suggesting that it may have been a centre of diversification.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    There is potential for extensive gene flow and the possibility of limited population structure in C. porosus.

    “Together, these observations indicate the potential for extensive gene flow and the possibility of limited population structure in C. porosus.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    Long-distance dispersal and historical sea-level changes were probably key drivers of the distribution of C. porosus.

    “Long-distance dispersal and historical sea-level changes were probably key drivers of its distribution.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    Measures were taken to avoid contamination and to cause minimal damage during sampling.

    “Measures were taken to avoid contamination and to cause minimal damage.”
    Quote in the paperNot a substantial claim
27 of 27

  • The authors state this as an assumption.

    The strict clock model, assuming a constant evolutionary rate among branches for each partition, is adequate for estimating divergence times.

    “using a strict clock model assuming a constant evolutionary rate among branches for each partition”

  • The paper relies on this without support.

    Nuclear genomic studies reveal strong regional differentiation in C. porosus.

    “consistent with nuclear genomic studies revealing strong regional differentiation”

  • The paper relies on this without support.

    The museum specimens' sampling locations are known and correct.

    “we sequenced mitochondrial genomes from museum specimens with known sampling locations”

  • The paper relies on this without support.

    Captive crocodiles previously removed from the wild and captive-bred crocodiles of C. porosus represent their source populations.

    “captive crocodiles previously removed from the wild and captive-bred crocodiles of C. porosus”

  • The paper relies on this without support.

    Mitochondrial DNA is maternally inherited and reflects only female-mediated gene flow.

    “Mitochondrial DNA, being maternally inherited, reflects only female-mediated gene flow.”

  • The paper relies on this without support.

    In species with male-biased dispersal, stronger population differentiation in mtDNA than in nuclear markers can result, potentially overlooking connectivity driven by males.

    “In species with male-biased dispersal, this can result in stronger population differentiation in mtDNA than in nuclear markers, potentially overlooking connectivity driven by males.”

  • The paper relies on this without support.

    The mitochondrial genome within Crocodylia is conservative.

    “Therefore, the limited mitochondrial differentiation observed here could mainly reflect the conservative nature of the mitochondrial genome within Crocodylia rather than showing evidence for the absence of population structure.”
7 of 7

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Two different ages for the Crocodylus crown group

    Major

    The most recent common ancestor of Crocodylus is the crown-group node, but it is dated to both 18.37 Ma and 24.54 Ma.

  • Sulawesi haplotype R is omitted from the Sulawesi count

    Minor

    The text says Sulawesi has three haplotypes, G-I, but also says haplotype R was found there. That makes at least four Sulawesi haplotypes.

2 of 2

Cites

Flagged first, then by citations

Research works printed but not linked: 10

  1. Whitaker, 2008, Who’s got the biggest, Crocodile Spec. Group Newsl., 27, 26
  2. Gerlach, 1994, On the crocodiles of the western Indian Ocean, Phelsuma, 2, 54
  3. Bour, 2022, Nikolaus Michael Oppel’s drawings, watercolors, and engravings. 3. Crocodiles (1807–1817), a comparative study of some historical and recent crocodile illustrations, Wahlgreniana, 1, 1
  4. González Fortes, 2019, Ancient DNA
  5. Huang, 2021, Protocol for cross-species target-gene enrichment, Bio, 101
  6. Chevreux, 1999, Genome sequence assembly using trace signals and additional sequence information, Comp. Sci. Biol.: Proc. GCB, 99, 45
  7. Sambrook, 1989, Molecular cloning: a laboratory manual
  8. Deraniyagala, 1953, A coloured atlas of some vertebrates from Ceylon. Tetrapod Reptilia, 101
  9. Deraniyagala, 1955, A new race of estuarine crocodile from Ceylon, Spolia Zeylan, 27, 277
  10. Wermuth, 1977, Das Tierreich, 1

Cited by

Sorted by citations

Authors
Agne, S., Arnold, P., Belle, B., Straube, N., Hofreiter, M., & Glaw, F.
Affiliations
  • University of Potsdam (DE)
  • Seychelles Natural History Museum 2 , ,
  • University of Bergen (NO)
  • Bavarian State Collection of Zoology (DE)
Corresponding author
Agne, Stefanie
ORCID
Venue
Royal Society Open Science
Publisher
The Royal Society
Published
2026-01-28
Volume
13
Issue
1
ISSN
2054-5703 (ISSN-L)
DOI
10.1098/rsos.251546
OpenAlex
W7125977380
Cited by
1
References
55
Citations by year
2026: 1
FWCI
3.97
Type
journal article
Language
en
Open access
Licence
Locations
Royal Society Open Science (publishedVersion, cc-by)
Funders
  • Deutsche Forschungsgemeinschaft
  • SNSB-innovativ
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
Crocodylus porosus, saltwater crocodile, Crocodylus niloticus, Crocodylus palustris, mitochondrial genome, museum specimens, population structure, haplotypes, mitochondrial DNA control region, genetic connectivity, crocodile conservation

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