The Evolution of Suidae

Frantz, Laurent; Meijaard, Erik; Gongora, Jaime; Haile, James; Groenen, Martien A. M.; Larson, Greger

doi:10.1146/annurev-animal-021815-111155

Cited by 106 publications

(118 citation statements)

References 117 publications

(179 reference statements)

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“…The divergence between the different Sus species is ∼4.2 MYA, whereas that of Sus with warthog is ca. 10 MYA (Frantz et al 2016). We removed those SNPs for which the ancestral allele could not be reliably identified or with less than two alleles.…”

Section: Methodsmentioning

confidence: 99%

A Pathway-Centered Analysis of Pig Domestication and Breeding in Eurasia

Leno-Colorado

Hudson

Reverter

et al. 2017

G3 Genes|Genomes|Genetics

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Ascertaining the molecular and physiological basis of domestication and breeding is an active area of research. Due to the current wide distribution of its wild ancestor, the wild boar, the pig (Sus scrofa) is an excellent model to study these processes, which occurred independently in East Asia and Europe ca. 9000 yr ago. Analyzing genome variability patterns in terms of metabolic pathways is attractive since it considers the impact of interrelated functions of genes, in contrast to genome-wide scans that treat genes or genome windows in isolation. To that end, we studied 40 wild boars and 123 domestic pig genomes from Asia and Europe when metabolic pathway was the unit of analysis. We computed statistical significance for differentiation (Fst) and linkage disequilibrium (nSL) statistics at the pathway level. In terms of Fst, we found 21 and 12 pathways significantly differentiated at a q-value < 0.05 in Asia and Europe, respectively; five were shared across continents. In Asia, we found six significant pathways related to behavior, which involved essential neurotransmitters like dopamine and serotonin. Several significant pathways were interrelated and shared a variable percentage of genes. There were 12 genes present in >10 significant pathways (in terms of Fst), comprising genes involved in the transduction of a large number of signals, like phospholipase PCLB1, which is expressed in the brain, or ITPR3, which has an important role in taste transduction. In terms of nSL, significant pathways were mainly related to reproductive performance (ovarian steroidogenesis), a similarly important target trait during domestication and modern animal breeding. Different levels of recombination cannot explain these results, since we found no correlation between Fst and recombination rate. However, we did find an increased ratio of deleterious mutations in domestic vs. wild populations, suggesting a relaxed functional constraint associated with the domestication and breeding processes. Purifying selection was, nevertheless, stronger in significantly differentiated pathways than in random pathways, mainly in Europe. We conclude that pathway analysis facilitates the biological interpretation of genome-wide studies. Notably, in the case of pig, behavior played an important role, among other physiological and developmental processes.

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Section: Methodsmentioning

confidence: 99%

A Pathway-Centered Analysis of Pig Domestication and Breeding in Eurasia

Leno-Colorado

Hudson

Reverter

et al. 2017

G3 Genes|Genomes|Genetics

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“…populations in East Asia and Anatolia were domesticated independently, and, like all major animal domesticates, pigs (Sus scrofa) are now (53,54). associated with humans well outside their natural Old World distribution (66). Dogs (Canis familiaris), the only animal domesticated before the emergence of agricultural societies, are now the most abundant and ubiquitous carnivore, with an estimated 700 million to 1 billion dogs worldwide (67).…”

Section: Four Key Phases Of Anthropogenic Transformationmentioning

confidence: 99%

Ecological consequences of human niche construction: Examining long-term anthropogenic shaping of global species distributions

Boivin

Zeder

Fuller

et al. 2016

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

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The exhibition of increasingly intensive and complex niche construction behaviors through time is a key feature of human evolution, culminating in the advanced capacity for ecosystem engineering exhibited by Homo sapiens. A crucial outcome of such behaviors has been the dramatic reshaping of the global biosphere, a transformation whose early origins are increasingly apparent from cumulative archaeological and paleoecological datasets. Such data suggest that, by the Late Pleistocene, humans had begun to engage in activities that have led to alterations in the distributions of a vast array of species across most, if not all, taxonomic groups. Changes to biodiversity have included extinctions, extirpations, and shifts in species composition, diversity, and community structure. We outline key examples of these changes, highlighting findings from the study of new datasets, like ancient DNA (aDNA), stable isotopes, and microfossils, as well as the application of new statistical and computational methods to datasets that have accumulated significantly in recent decades. We focus on four major phases that witnessed broad anthropogenic alterations to biodiversity-the Late Pleistocene global human expansion, the Neolithic spread of agriculture, the era of island colonization, and the emergence of early urbanized societies and commercial networks. Archaeological evidence documents millennia of anthropogenic transformations that have created novel ecosystems around the world. This record has implications for ecological and evolutionary research, conservation strategies, and the maintenance of ecosystem services, pointing to a significant need for broader cross-disciplinary engagement between archaeology and the biological and environmental sciences.biodiversity | extinctions | invasive species | novel ecosystems | Anthropocene The reshaping of global biodiversity is one of the most significant impacts humans have had on Earth's ecosystems. As our planet experiences its sixth "mass extinction event" (1), the effect of anthropogenic landscape modification, habitat fragmentation, overexploitation, and species invasions could not be more apparent (2, 3). These transformations are linked largely to the industrial economies, burgeoning populations, and dense transport networks of contemporary human societies. Accordingly, the humanmediated alteration of species distributions has been characterized as a modern phenomenon with limited, and largely insignificant, historical antecedents. This conventional understanding fails to account for several decades of archaeological, paleoecological, and genetic research that reveal a long and widespread history of human transformation of global biodiversity (4-6). The evolutionary trajectory of Homo sapiens has seen growing capacities for advanced cognition and demographic and geographic expansion, along with an exponential increase in the scope and impact of human niche constructing activities (7) that have culminated in fundamental changes to planetary ecosystems.Drawing upon findings from ...

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“…It represents a "ghost lineage" since there are no closely related extant species outside Sulawesi (e.g. African suids are more closely related to the Babirusa than Asian suids) and the Babirusa is unknown in the fossil record outside Sulawesi [24]. Three extant species of Babirusa (distributed primarily in the interior of Sulawesi and on surrounding islands [21][22][23] have been described: Babyrousa babyrousa (Buru and Sulu islands), Babyrousa celebensis (mainland Sulawesi) and Babyrousa togeanensis (Togian Island) [25].…”

Section: Introductionmentioning

confidence: 99%

“…In contrast with Anoa and Babirusa, the Sulawesi warty pig (SWP; Sus celebensis) occupies a wide range of habitats, ranging from swamps to rainforests. This species is closely related to the Eurasian wild pig(Sus scrofa), from which it diverged during the early Pleistocene (~2 Myr ago) [24,30].…”

Section: Introductionmentioning

confidence: 99%

Synchronous diversification of Sulawesi’s iconic artiodactyls driven by recent geological events

Frantz

Rudzinski

Nugraha

et al. 2018

Preprint

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The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back 40 Myr ago. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that recent uplift of previously submerged portions of land on Sulawesi promoted diversification, and that much of the its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric data sets derived from Sulawesi's three largest mammals: the Babirusa, Anoa, and Sulawesi warty pig.Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Myr ago to 2-3 Myr ago), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that recent emergence of land on Sulawesi (~1-2 Myr) may have allowed species to expand synchronously. Altogether, our results indicates that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.

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The Evolution of Suidae

Cited by 106 publications

References 117 publications

A Pathway-Centered Analysis of Pig Domestication and Breeding in Eurasia

A Pathway-Centered Analysis of Pig Domestication and Breeding in Eurasia

Ecological consequences of human niche construction: Examining long-term anthropogenic shaping of global species distributions

Synchronous diversification of Sulawesi’s iconic artiodactyls driven by recent geological events

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