Molecular Genetics Unveiled Unknown Family Relationships and Hybrids in an Ex-Situ Colony of African Penguins (Spheniscus demersus)

Probably not a substantial claim: may not pass S2 (checkable).

There is a need to develop methods and practical computing tools to analyze pedigrees in order to maintain genetic diversity of ex situ population, main goal of an ex situ breeding program.

“Especially in group-living species, in which pedigree analysis for the genetic management is far from being trivial, there is a need to develop methods and practical computing tools to analyze pedigrees in order to maintain genetic diversity of the ex situ population, main goal of an ex situ breeding program (Jiménez-Mena et al. 2016).”

• cites Jiménez-Mena et al. 2016 sourceSupported

Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).

Knowledge of the frequency of extra-pair paternity in colonially nesting species may have implications for the genetic management of captive avian populations.

“Knowledge of the frequency of extra-pair paternity in colonially nesting species may have implications for the genetic management of captive avian populations (Ferrie et al. 2013).”

• cites Ferrie et al. 2013 sourceSupported

May combine two claims.

Previous studies proved that the FL method is the most accurate and that COLONY outperforms other commonly used software in carrying out parentage analysis.

“Actually, previous studies proved that the FL method is the most accurate (Wang 2004(Wang , 2012;;Wang and Santure 2009) and that COLONY outperforms other commonly used software in carrying out parentage analysis (Wang 2012;Ferrie et al. 2013;Harrison et al. 2013).”

• cites Wang 2004 sourceNot checked — no full text of the source
• cites Wang 2012 sourcePartly supported

  The Marker information section reports that FL outperformed LS and PL in the parentage comparisons, supporting the claim about FL's accuracy within those tests. The Evaluation of the Method section says FL was implemented in COLONY2, but the paper does not establish that COLONY outperforms other commonly used software for parentage analysis; it compares methods rather than software packages. Page numbers are unavailable in our copy. (LLM, conf=0.87)

  Experimental — accuracy not yet measured
• cites Ferrie et al. 2013 sourceCould not verify

  The indexed study summary (page not provided) says COLONY helped reconstruct parentage and improve the marabou stork studbook. It does not compare COLONY with other parentage-analysis software; searches for software comparisons and relative accuracy found no such passage. The separate FL-method claim is attributed to other citations, not Ferrie et al. (LLM, conf=0.72)

  Experimental — accuracy not yet measured

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

In captivity, hybrids between Humboldt and Magellanic penguins, Humboldt and African penguins, and African and Magellanic penguins are reported.

“In captivity, hybrids between Humboldt and Magellanic penguins, Humboldt and African penguins, and African and Magellanic penguins are reported (Thumser and Karron 1994;McCarthy 2006;Simeone et al. 2009).”

• cites Thumser and Karron 1994 sourceNot checked — no full text of the source
• cites McCarthy 2006Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

• cites Simeone et al. 2009 sourcePartly supported

  The introduction reports captive interbreeding between Humboldt and Magellanic penguins, including fertile offspring. The Results report two captive Humboldt–African hybrids. Our copy does not report captive African–Magellanic hybrids, so it supports only two of the three pairings attributed to this paper. (LLM, conf=0.87)

  Experimental — accuracy not yet measured

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

The genus Spheniscus comprises two more extant species besides Humboldt and African penguins: the Magellanic penguin and the Galapagos penguin.

“The genus Spheniscus comprises 2 more extant species, other than Humboldt and African penguins: the Magellanic penguin (S. magellanicus) and the Galapagos penguin (S. mendiculus) (Ksepka and Thomas, 2012).”

• cites Ksepka and Thomas, 2012 sourcePartly supported

  The Results (page unavailable) state that Spheniscus has four extant species and identify S. magellanicus as the sister species of the African penguin, S. demersus. Our copy does not identify the other two extant species as the Humboldt and Galapagos penguins, so it does not fully support the cited species list. (LLM, conf=0.84)

  Experimental — accuracy not yet measured

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

Based on molecular and morphological data, Galapagos and Humboldt penguins are considered sister species, as are Magellanic and African penguins.

“Based on molecular and morphological dataset, Galapagos and Humboldt penguins are considered sister species, as are Magellanic and African penguins (Ksepka and Thomas 2012).”

• cites Ksepka and Thomas 2012 sourcePartly supported

  The Methods describe an analysis combining morphological and molecular data, and the Results explicitly call African penguins (S. demersus) and Magellanic penguins (S. magellanicus) sister species. The passages in our copy do not establish the claimed sister relationship between Galápagos and Humboldt penguins. (LLM, conf=0.86)

  Experimental — accuracy not yet measured

May combine two claims.

Out of 29 maternity kinships reported in the studbook, 17 were confirmed by the software with a probability >95%, 5 with relaxed confidence, and 7 with low confidence.

“Out of 29 maternity kinships reported in the studbook, 17 were confirmed by the software with a probability >95%, 5 with relaxed confidence, and 7 with low confidence.”

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

Only 1 marker (PNN07) showed absence of amplification in 2 samples (Ice and Picchio).

“Only 1 marker (PNN07) showed the absence of amplification in 2 samples (Ice and Picchio).”

May combine two claims.

The sexing protocol produced a 364-bp fragment of the CHD gene in male samples and two fragments (364 bp and 380 bp) in female samples.

“Following our protocol, PCR reaction on male samples produced a 364-bp fragment of the CHD gene and showed a single peak after capillary electrophoresis; female samples were characterized by 2 CHD gene fragments of different length (364 bp and 380 bp) with 2 peaks in the electropherogram.”

May combine two claims.

Neither Fis values calculated for each marker nor that of the whole population showed a statistically significant P value (P < 0.05).

“Neither Fis values calculated for each marker nor that of the whole population showed a statistically significant P value (P < 0.05).”

May combine two claims.

Sex assigned by keepers was confirmed in 25 other animals, and was wrong in one case: Zin, considered a male, was found to be female.

“Sex assigned by keepers was confirmed in 25 other animals, which proved wrong in one case: the penguin named Zin, considered a male, was found to be female.”

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

Only 5 markers showed a PIC less than 0.5.

“Only 5 markers showed a PIC less than 0.5 (B3-2; PNN05; PNN07; Sh2Ca22; Em6.2).”

May combine two claims.

Of the 26 microsatellites tested for kinship, 7 showed no positive amplification and 4 were monomorphic and excluded from further analyses.

“Of the 26 microsatellites tested for kinship, 7 (PNN03, Sh2Ca21, G2-2, G3-6, M1-11, and EMM1 EMM3) showed no positive amplification in our samples, whereas 4 (H2-6, Em2, EMM2 and EMM5) were monomorphic and excluded from further analyses.”

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

Frequency of the null allele ranged from -0.075 to 0.085 and was considered irrelevant.

“Frequency of the null allele ranged from -0.075 to 0.085 and was considered irrelevant.”

May combine two claims.

Out of 26 full-sib pairs, 14 were confirmed with strict confidence, 2 with relaxed confidence, 8 with low confidence, and 2 full-sibs pairs were not confirmed.

“Out of 26 full-sib pairs, 14 were confirmed with strict confidence, 2 with relaxed confidence, 8 with low confidence, and 2 full-sibs pairs were not confirmed (Tables 2 and 3, and Supplementary Figure 1S).”

May combine two claims.

Genetic data indicate that Amadi is more likely Isa's mother (96% probability) rather than his sister (68% probability), and best configuration analysis confirmed this likelihood.

“Genetic data highlighted that Amadi is more likely Isa's mother (96% probability) rather than his sister (68% probability) and best configuration analysis confirmed this likelihood.”

May combine two claims.

These alleles allowed Umbo's assignment to his progeny (2 sons and 1 grandson), even if their mtDNA was found to have a similarity of 99% with sequences of S. demersus.

“These alleles allowed Umbo's assignment to his progeny (2 sons and 1 grandson), even if their mtDNA was found to have a similarity of 99% with sequences of S. demersus.”

May combine two claims.

The cytb sequence obtained from Umbo's DNA showed a similarity of 99% with Humboldt penguin sequences deposited in GenBank, showing that Umbo belongs, at least for the maternal line, to the S. humboldti species.

“The cytb sequence obtained from Umbo's DNA showed a similarity of 99% with Humboldt penguin sequences deposited in GenBank, showing that Umbo belongs, at least for the maternal line, to the S. humboldti species.”

May combine two claims.

Genetic analysis revealed extra-pair copulations, same-sex couples, and hybrids S. spheniscus × S. humboldti in the colony.

“Genetic analysis allowed us to highlight aspects of species biology that are hard to assess by observations: extra-pair copulations, same sex couples, and hybrids S. spheniscus × S. humboldti.”

May combine two claims.

Out of the 28 paternity relationships reported in the studbook, 12 were confirmed with a probability >95%, 4 with relaxed confidence, and 5 with low confidence.

“Out of the 28 paternity relationships reported in the studbook, 12 were confirmed with a probability >95%, 4 with relaxed confidence, and 5 with low confidence.”

May combine two claims.

In the group studied, some individuals showed African penguin phenotypic aspects but had both S. humboldti mitochondrial DNA and nuclear markers that could be private alleles of S. humboldti.

“In the group studied here, some individuals showed African penguin phenotypical aspects but had both S. humboldti mitochondrial DNA and nuclear markers that could be private alleles of S. humboldti.”

May combine two claims.

During the 16-month observation period, 4 episodes of infidelity were recorded by field observations, and parentage genetic analysis confirmed extra-pair copulation in 3 cases.

“During the 16-month observation period, 4 episodes of infidelity were recorded by field observations and parentage genetic analysis of the offspring confirmed extra-pair copulation in 3 cases.”

May combine two claims.

Using only molecular data (sex and genotype) and age information, 89% of the parentage relationships were reconstructed and 11% of the studbook data were not confirmed.

“Using only molecular data (sex and genotype) and age information, 89% of the parentage relationships were reconstructed and 11% of the studbook data were not confirmed.”

May combine two claims.

Molecular methods can be effectively employed to identify unknown parentage relationships, assess presence of hybrids, assign sex, and verify accuracy of existing pedigrees.

“Molecular methods could help to reduce uncertainty since they can be effectively employed to: 1) identify unknown parentage relationships; 2) assess the presence of hybrids; 3) assign sex to the components of the colony; and 4) verify the accuracy of the existing pedigrees.”

Classified as probably not a substantial claim.

Studbook data were systematically used to exclude paternity and maternity on the basis of date of birth, date of death, and date of relocation.

“Studbook data were systematically used to exclude paternity and maternity on the basis of date of birth, date of death, and date of relocation (i.e., offspring had to have been born after parents but before the death of the putative parent and at the same institution).”

Probably not a substantial claim: may not pass S2 (checkable). May combine two claims.

Our findings provide new baseline knowledge about ethology and mating behavior of African penguins that have important implications for correct management and breeding of these seabirds in captivity, and provide a valuable contribution to studies in other captive populations.

“Our findings provide new baseline knowledge about ethology and mating behavior of African penguins that have important implications for the correct management and breeding of these seabirds in captivity, and provide a valuable contribution to studies in other captive populations.”

Classified as probably not a substantial claim.

Homozygous samples were amplified 3 times to limit the large allele drop-out effect.

“Homozygous samples were amplified 3 times to limit the large allele drop-out effect.”

Classified as probably not a substantial claim.

Accurate pedigrees yield essential information on inbreeding, kinships among individuals, and the distribution of individual founder contributions to a population.

“Accurate pedigrees yield essential information on inbreeding, kinships among individuals, and the distribution of individual founder contributions to a population (Ivy and Lacy 2010).”

• cites Ivy and Lacy 2010 sourceNot checked — no full text of the source

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

Several penguin species have sometimes been hosted in the same enclosures, and this practice may have led to mating between 2 species and to the spread of hybrid subjects.

“The Manual calls attention to the fact that several penguin species have sometimes been hosted in the same enclosures.This unwise practice may have led to the mating (also extra-pair mating) between 2 species and to the spread of hybrid subjects.”

• cites Schneider et al. 2014Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

May combine two claims.

When reconstructed consistently among runs, sibship and parentage were considered reliably inferred and taken into account to confirm colony pedigree.

“When reconstructed consistently among runs, sibship and parentage were considered reliably inferred and taken into account to confirm colony pedigree.”

May combine two claims.

Our approach allowed us to highlight aspects of species biology (extra-pair fertilizations, polygamy, cuckoldry) important for natural populations and to disclose potential problem of hybrids particularly important if ex situ population is considered a source of integration or restoration of populations in situ.

“Moreover, our approach allowed us to highlight aspects of species biology (i.e., extra-pair fertilizations, polygamy, cuckoldry) important for natural populations and to disclose the potential problem of hybrids particularly important if the ex situ population is considered a source of integration or restoration of populations in situ.”

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

A reaction without any DNA was added as negative control to each run to assess absence of contamination.

“A reaction without any DNA was added as negative control to each run to assess absence of contamination.”

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

Multiple runs with 3 different random number seeds were performed to check/confirm software output reliability, as suggested by Wang (2004).

“Since the dataset was small and included families assumed to be very small (1 to 3 offspring per sibship), multiple runs with 3 different random number seeds were performed to check/confirm software output reliability, as suggested by Wang (2004).”

• cites Wang (2004) sourceNot checked — no full text of the source

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

Between 80% and 90% of penguins in the wild retain the same mate at each mating season.

“Indeed, between 80% and 90% of penguins in the wild retain the same mate at each mating season (Randall 1983).”

• cites Randall 1983Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

May combine two claims.

In this case, one female of the couple paired with a male and then hatched the egg with another female.

“In this case, one female of the couple paired with a male and then hatched the egg with another female.”

May combine two claims.

These individuals could be a first generation of hybrids or a backcross from an F1 with African penguin.

“Accordingly, they could be a first generation of hybrids or a backcross from a F1 with African penguin.”

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

The kinship analysis performed in this study is the first to be carried out in a colony of African penguins housed in a European zoo.

“The kinship analysis we performed is the first to be carried out in a colony of African penguins housed in a European zoo (Valentina Isaja, member of the EEP African Penguin Committee; personal communication).”

Probably not a substantial claim: may not pass S2 (checkable). May combine two claims.

Strict adherence to genetic data is not recommendable because besides scoring or sequencing errors, other limitations in the use of genetic data for parentage assignment can emerge when sampling of potential parents is incomplete or homozygosity reduces the informativeness of the markers.

“Nonetheless, strict adherence to genetic data is not recommendable: besides scoring or sequencing errors, other limitations in the use of genetic data for parentage assignment can emerge when sampling of potential parents is incomplete or homozygosity reduces the informativeness of the markers.”

May combine two claims.

The penguins display no phenotypical characters of S. humboldti species and are probably hybrids.

“The penguins display no phenotypical characters of S. humboldti species and are probably hybrids.”

Probably not a substantial claim: may not pass S2 (checkable).

Our analysis of a colony of African penguins addresses the need to combine molecular data with observational and studbook information in the management of captive animal populations.

“In conclusion, our analysis of a colony of African penguins addresses the need to combine molecular data with observational and studbook information in the management of captive animal populations (Fienieg and Galbusera 2013).”

• cites Fienieg and Galbusera 2013 sourceNot checked — no full text of the source

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

Humboldt x African hybrids are considered quite common and recognized as partially fertile, since some individuals are known to have had offspring.

“In particular, Humboldt x African hybrids are considered quite common and recognized as partially fertile, since some individuals are known to have had offspring (McCarthy 2006).”

• cites McCarthy 2006Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

May combine two claims.

All unknown relationships, although assigned with a probability between 80% and 90%, were confirmed by comparing the offspring's and parents' genotypes and by the best configuration obtained using maximum likelihood analysis.

“All unknown relationships, although assigned with a probability between 80% and 90%, were confirmed by comparing the offspring's and parents' genotypes and by the best configuration obtained using maximum likelihood analysis.”

Probably not a substantial claim: may not pass S2 (checkable).

In such circumstances, molecular methods could provide a useful tool for testing studbook records.

“In such circumstances, molecular methods could provide a useful tool for testing studbook records.”

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

Of the studies on extra-pair copulation in penguins, only the study by Sakaoka and colleagues was conducted on captive animals.

“Of these studies, only that by Sakaoka and colleagues was conducted on captive animals.”

• cites Sakaoka et al. 2014 sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S2 (checkable).

Unravelling the mating system of a species is essential for successful breeding, captive management, and conservation programs.

“Unravelling the mating system of a species is essential for successful breeding, captive management, and conservation programs (Miño et al. 2009).”

• cites Miño et al. 2009Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based). May combine two claims.

Low founder number is associated with high homozygosity in offspring, which might explain the absence or low probability of paternity assignment to the candidate father.

“founders is low, a high homozygosity in offspring could be observed and might explain the absence (or a low probability) of paternity assignment to the candidate father.”

Probably not a substantial claim: may not pass S1 (asserted). May combine two claims.

We hypothesized a documental error or an incorrect assignment to the same mating pair in the zoo of origin.

“We hypothesized a documental error or an incorrect assignment to the same mating pair in the zoo of origin.”

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

Extra-pair copulation has been described in Humboldt penguins and Adélie penguins.

“Although long believed a monogamous species, extra-pair copulation has been described in different penguin species: the Humboldt penguin (Spheniscus humboldti; Schwartz et al. 1999) and the Adélie penguin (Pygoscelis adeliae; Hunter et al. 1995;Hunter and Davis 1998;Pilastro et al. 2001;Sakaoka et al. 2014).”

• cites Schwartz et al. 1999 sourceNot checked — no full text of the source
• cites Hunter et al. 1995 sourceNot checked — no full text of the source
• cites Sakaoka et al. 2014 sourceNot checked — no full text of the source

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

When the number of founders is low, a high homozygosity in offspring could be observed and might explain the absence (or a low probability) of paternity assignment.

“Moreover, when the number of founders is low, a high homozygosity in offspring could be observed and might explain the absence (or a low probability) of paternity assignment to”