A new genus of horse from Pleistocene North America

Heintzman, Peter D.; Zazula, Grant D.; MacPhee, R. D. E.; Scott, Eric; Cahill, James A.; McHorse, Brianna K.; Kapp, Joshua D.; Stiller, Mathias; Wooller, Matthew J.; Orlando, Ludovic; Southon, John; Froese, Duane G.; Shapiro, Beth

doi:10.7554/elife.29944

Cited by 66 publications

(83 citation statements)

References 80 publications

(191 reference statements)

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“…These characteristics of ancient DNA and practices used in palaeogenomic studies make them particularly vulnerable to reference bias (Prüfer et al ., 2010; Schubert et al ., 2012). It has been shown that pseudo-haploid data can be more biased than imputed genotypes (Martiniano et al ., 2017), and that reference bias and fragment length artifacts can interfere with phylogenetic classifications (Heintzman et al ., 2017). Reference bias can influence downstream analyses if these are based on estimating allele frequencies in a population, or studying pairwise allele sharing between individuals and groups.…”

Section: Introductionmentioning

confidence: 99%

“…Sequencing reads carrying an alternative allele will naturally have mismatches in the alignment to the reference genome and consequently have lower mapping scores than reads carrying the same allele as the reference. This effect increases with genetic distance from the reference genome, which is of particular interest when using a reference genome from a related species for mapping (Shapiro and Hofreiter, 2014; Gopalakrishnan et al, 2017; Heintzman et al, 2017). Generally, reference bias can influence variant calling by missing alternative alleles or by wrongly calling heterozygous sites as homozygous reference (Bobo et al, 2016; Ros-Freixedes et al, 2018) which is known to influence estimates of heterozygosity and allele frequencies (Chen et al, 2012; Bryc et al, 2013; Brandt et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

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The presence and impact of reference bias on population genomic studies of prehistoric human populations

Günther

Nettelblad

2018

Preprint

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High quality reference genomes are an important resource in genomic research projects. A consequence is that DNA fragments carrying the reference allele will be more likely to map successfully, or receive higher quality scores. This reference bias can have effects on downstream population genomic analysis when heterozygous sites are falsely considered homozygous for the reference allele.In palaeogenomic studies of human populations, mapping against the human reference genome is used to identify endogenous human sequences. Ancient DNA studies usually operate with low sequencing coverages and fragmentation of DNA molecules causes a large proportion of the sequenced fragments to be shorter than 50 bp -reducing the amount of accepted mismatches, and increasing the probability of multiple matching sites in the genome. These ancient DNA specific properties are potentially exacerbating the impact of reference bias on downstream analyses, especially since most studies of ancient human populations use pseudohaploid data, i.e. they randomly sample only one sequencing read per site.We show that reference bias is pervasive in published ancient DNA sequence data of prehistoric humans with some differences between individual genomic regions. We illustrate that the strength of reference bias is negatively correlated with fragment length. Reference bias can cause differences in the results of downstream analyses such as population affinities, heterozygosity estimates and estimates of archaic ancestry. These spurious results highlight how important it is to be aware of these technical artifacts and that we need strategies to mitigate the effect. Therefore, we suggest some post-mapping filtering strategies to resolve reference bias which help to reduce its impact substantially.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The presence and impact of reference bias on population genomic studies of prehistoric human populations

Günther

Nettelblad

2018

Preprint

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“…Moreover, new approaches to age-depth modeling provide better estimates of temporal certainty for unsampled portions of sedimentary deposits (Buck et al 1999, Haslett and Parnell 2008, Bronk Ramsey 2009, Blaauw and Christeny 2011. Second, ancient DNA has been crucial for improving our ability to obtain species-level identifications from fossil assemblages (Heintzman et al 2017) and extending the variety of taxa that could be sampled from sedimentary deposits (Pedersen et al 2015).…”

Section: Inferring Assemblage-level Processes In Space and Time: Datamentioning

confidence: 99%

Understanding ecological change across large spatial, temporal and taxonomic scales: integrating data and methods in light of theory

Rapacciuolo

Blois

2019

Ecography

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Ecography E4 awardThe difficulty of integrating multiple theories, data and methods has slowed progress towards making unified inferences of ecological change generalizable across large spatial, temporal and taxonomic scales. However, recent progress towards a theoretical synthesis now provides a guiding framework for organizing and integrating all primary data and methods for spatiotemporal assemblage-level inference in ecology. In this paper, we describe how recent theoretical developments can provide an organizing paradigm for linking advances in data collection and methodological frameworks across disparate ecological sub-disciplines and across large spatial and temporal scales. First, we summarize the set of fundamental processes that determine change in multispecies assemblages across spatial and temporal scales by reviewing recent theoretical syntheses of community ecology. Second, we review recent advances in data and methods across the main sub-disciplines concerned with ecological inference across large spatial, temporal and taxonomic scales, and organize them based on the primary fundamental processes they include, rather than the spatiotemporal scale of their inferences. Finally, we highlight how iteratively focusing on only one fundamental process at a time, but combining all relevant spatiotemporal data and methods, may reduce the conceptual challenges to integration among ecological sub-disciplines. Moreover, we discuss a number of avenues for decreasing the practical barriers to integration among data and methods. We aim to reconcile the recent convergence of decades of thinking in community ecology and macroecology theory with the rapid progress in spatiotemporal approaches for assemblage-level inference, at a time where a robust understanding of spatiotemporal change in ecological assemblages is more crucial than ever to conserve biodiversity.

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“…Since we evaluated morphological characters of teeth and bones of fossil horses from southern Mexico and to avoid the unnecessary proliferation of names for the Mexican equid species, we follow the taxonomic scheme of Priego-Vargas et al (2017, table 10) that recognized four Pleistocene Equus species for Mexico: Equus conversidens, E. mexicanus, E. francisci, and E. cedralensis. Since Heintzman et al (2017) transferred E. francisci to Haringtonhippus, instead of E. francisci, we used the name H. francisci.…”

Section: Studied Specimensmentioning

confidence: 99%

“…By means of paleogenomic and morphometric analyses, a new genus of NWSL horse for the Pleistocene of North America was erected: Haringtonhippus francisci. This species was reported (as Equus conversidens) from San Josecito Cave, Nuevo Léon, based upon a short mitochondrial DNA sequence (Barrón-Ortiz et al, 2017); this record was subsumed into H. francisci by Heintzman et al (2017). Finally, Barrón-Ortiz et al (2019) based on a morphology-based tree, determined that Equus comprises eight species, including H. francisci, and suggested that Haringtonhippus should be considered a synonym of Equus, but the authors do not formally synonymize both taxa.…”

Section: Introductionmentioning

confidence: 99%

Species Diversity and Paleoecology of Late Pleistocene Horses From Southern Mexico

Jiménez-Hidalgo¹,

Carbot-Chanona²,

Guerrero-Arenas³

et al. 2019

Front. Ecol. Evol.

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Equids are among the most common mammals found in faunal assemblages of Late Pleistocene age in Mexico. Much of what is known about the Equus species is the result of studies conducted in central and northern Mexico; much less is known about species in lower latitudes of Mexico. Here we describe three species that inhabited Oaxaca and Chiapas states. The fossil localities are in northwestern and central Oaxaca, as well as the central part of Chiapas. In Oaxaca, the largest species, Equus mexicanus, and the medium-sized Equus conversidens are represented by mandibles, skulls, diverse isolated teeth and some postcranial bones, while the smallest species, Haringtonhippus francisci is represented by a skull fragment and few isolated teeth. In Chiapas, E. mexicanus is represented by a mandible and several isolated teeth, E. conversidens by several mandibles and diverse isolated teeth, and H. francisci by isolated teeth and two mandibles. AMS radiocarbon and uranium dating of some of the equid localities in Oaxaca and Chiapas indicate that they were at least present since ∼44,000 Cal BP years, they were common around 30,000 Cal BP years, and were still present at the end of the Pleistocene, around 12,000 years ago. The record of H. francisci from Chiapas is the youngest in North America. A cluster analysis of extended mesowear data and a discriminant analysis showed that Equus conversidens from Chiapas was obligate grazer, whilst the rest of the equids were variable grazers. Geographic distribution of localities in southern Mexico indicates that during the Pleistocene the equid species moved across the Transvolcanic Belt-Sierra Madre del Sur temperate biogeographic corridor and the Tamaulipas-Central America Gulf Lowlands tropical corridor.

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A new genus of horse from Pleistocene North America

Cited by 66 publications

References 80 publications

The presence and impact of reference bias on population genomic studies of prehistoric human populations

The presence and impact of reference bias on population genomic studies of prehistoric human populations

Understanding ecological change across large spatial, temporal and taxonomic scales: integrating data and methods in light of theory

Species Diversity and Paleoecology of Late Pleistocene Horses From Southern Mexico

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