Novel opsin gene variation in large-bodied, diurnal lemurs

Some primate populations include both trichromatic and dichromatic (red-green colour blind) individuals due to allelic variation at the X-linked opsin locus. This polymorphic trichromacy is well described in day-active New World monkeys. Less is known about colour vision in Malagasy lemurs, but, unlike New World monkeys, only some day-active lemurs are polymorphic, while others are dichromatic. The evolutionary pressures underlying these differences in lemurs are unknown, but aspects of species ecology, including variation in activity pattern, are hypothesized to play a role. Limited data on X-linked opsin variation in lemurs make such hypotheses difficult to evaluate. We provide the first detailed examination of X-linked opsin variation across a lemur clade (Indriidae). We sequenced the X-linked opsin in the most strictly diurnal and largest extant lemur, Indri indri, and nine species of smaller, generally diurnal indriids (Propithecus). Although nocturnal Avahi (sister taxon to Propithecus) lacks a polymorphism, at least eight species of diurnal indriids have two or more X-linked opsin alleles. Four rainforest-living taxa-I. indri and the three largest Propithecus species-have alleles not previously documented in lemurs. Moreover, we identified at least three opsin alleles in Indri with peak spectral sensitivities similar to some New World monkeys

Data from: Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

Background: The greater bamboo lemur (Prolemur simus) is a member of the Family Lemuridae that is unique in their dependency on bamboo as a primary food source. This Critically Endangered species lives in small forest patches in eastern Madagascar, occupying a fraction of its historical range. Here we sequence the genome of the greater bamboo lemur for the first time, and provide genome resources for future studies of this species that can be applied across its distribution. Results: Following whole genome sequencing of five individuals we identified over 152,000 polymorphic single nucleotide variants (SNVs), and evaluated geographic structuring across nearly 19k SNVs. We characterized a stronger signal associated with a north-south divide than across elevations for our limited samples. We also evaluated the demographic history of this species, and infer a dramatic population crash. This species had the largest effective population size (estimated between ~900,000 to one million individuals) between approximately 60,000-90,000 years before present (ybp), during a time in which global climate change affected terrestrial mammals worldwide. We also note the single sample from the northern portion of the extant range had the largest effective population size around 35,000 ybp. Conclusions: From our whole genome sequencing we recovered an average genomic heterozygosity of 0.0037%, comparable to other lemurs. Our demographic history reconstructions recovered a probable climate-related decline (60-90,000 ybp), followed by a second population decrease following human colonization, which has reduced the species to a census size of approximately 1,000 individuals. The historical distribution was likely a vast portion of Madagascar, minimally estimated at 44,259 km2, while the contemporary distribution is only ~1,700 km2. The decline in effective population size of 89-99.9% corresponded to a vast range retraction. Conservation management of this species is crucial to retain genetic diversity across the remaining isolated populations

Data from: Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

Background: The greater bamboo lemur (Prolemur simus) is a member of the Family Lemuridae that is unique in their dependency on bamboo as a primary food source. This Critically Endangered species lives in small forest patches in eastern Madagascar, occupying a fraction of its historical range. Here we sequence the genome of the greater bamboo lemur for the first time, and provide genome resources for future studies of this species that can be applied across its distribution. Results: Following whole genome sequencing of five individuals we identified over 152,000 polymorphic single nucleotide variants (SNVs), and evaluated geographic structuring across nearly 19k SNVs. We characterized a stronger signal associated with a north-south divide than across elevations for our limited samples. We also evaluated the demographic history of this species, and infer a dramatic population crash. This species had the largest effective population size (estimated between ~900,000 to one million individuals) between approximately 60,000-90,000 years before present (ybp), during a time in which global climate change affected terrestrial mammals worldwide. We also note the single sample from the northern portion of the extant range had the largest effective population size around 35,000 ybp. Conclusions: From our whole genome sequencing we recovered an average genomic heterozygosity of 0.0037%, comparable to other lemurs. Our demographic history reconstructions recovered a probable climate-related decline (60-90,000 ybp), followed by a second population decrease following human colonization, which has reduced the species to a census size of approximately 1,000 individuals. The historical distribution was likely a vast portion of Madagascar, minimally estimated at 44,259 km2, while the contemporary distribution is only ~1,700 km2. The decline in effective population size of 89-99.9% corresponded to a vast range retraction. Conservation management of this species is crucial to retain genetic diversity across the remaining isolated populations

The mesocolon a histological and electron microscopic characterization of the mesenteric attachment of the colon prior to and after surgical mobilization

Background: Colonic mobilization requires separation of mesocolon from underlying fascia. Despite the surgical importance of planes formed by these structures, no study has formally characterized their microscopic features. The aim of this study was to determine the histological and electron microscopic appearance of mesocolon, fascia, and retroperitoneum, prior to and after colonic mobilization.Methods: In 24 cadavers, samples were taken from right, transverse, descending, and sigmoid mesocolon. In 12 cadavers, specimens were stained with hematoxylin and eosin (3 sections) or Masson trichrome (3 sections). In the second 12 cadavers, lymphatic channels were identified by staining immunohistochemically for podoplanin. The ascending mesocolon was assessed with scanning electron microscopy. The above process was first conducted with the mesocolon in situ. The mesocolon was then surgically mobilized, and the process was repeated on remaining structures.Results: The microscopic structure of mesocolon and associated fascia was consistent from ileocecal to mesorectal level. A surface mesothelium and underlying connective tissue were evident throughout. Fibrous septae separated adipocyte lobules. Where apposed to retroperitoneum, 2 mesothelial layers separated mesocolon and underlying retroperitoneum. A connective tissue layer occurred between these (ie, Toldt's fascia). Lymphatic channels were evident both in mesocolic connective tissue and Toldt's fascia. After surgical separation of mesocolon and fascia both remained contiguous, the fascia remained in situ and the retroperitoneum undisturbed.Conclusions: The findings demonstrate that the contiguous mesocolon and retroperitoneum are separated by mesothelial and connective tissue layers. These properties generate the surgical planes (ie, meso-and retrofascial planes) exploited in colonic and mesocolic mobilization

Data from: Novel opsin gene variation in large-bodied, diurnal lemurs

Some primate populations include both trichromatic and dichromatic (red–green colour blind) individuals due to allelic variation at the X-linked opsin locus. This polymorphic trichromacy is well described in day-active New World monkeys. Less is known about colour vision in Malagasy lemurs, but, unlike New World monkeys, only some day-active lemurs are polymorphic, while others are dichromatic. The evolutionary pressures underlying these differences in lemurs are unknown, but aspects of species ecology, including variation in activity pattern, are hypothesized to play a role. Limited data on X-linked opsin variation in lemurs make such hypotheses difficult to evaluate. We provide the first detailed examination of X-linked opsin variation across a lemur clade (Indriidae). We sequenced the X-linked opsin in the most strictly diurnal and largest extant lemur, Indri indri, and nine species of smaller, generally diurnal indriids (Propithecus). Although nocturnal Avahi (sister taxon to Propithecus) lacks a polymorphism, at least eight species of diurnal indriids have two or more X-linked opsin alleles. Four rainforest-living taxa—I. indri and the three largest Propithecus species—have alleles not previously documented in lemurs. Moreover, we identified at least three opsin alleles in Indri with peak spectral sensitivities similar to some New World monkeys

Sequence data for exons 3 and 5 of the X-linked opsin gene (Indriidae)

Sequence alignments for exons 3 and 5 of the X-linked opsin gene. Data include consensus sequences for ten species of Indriidae. Alignments were generated in Geneious. The three key functional sites (180: exon 3, 277 and 285: exon 5) are highlighted (added in Adobe Illustrator)

Nucleotide alignment for exon 3 of the X-linked opsin gene (Indriidae)

Nucleotide alignment of consensus sequences for exon 3 of the X-linked opsin gene (Plain Text file in FASTA format generated in Geneious). Sequences represent 10 species of Indriidae

Supplementary Materials: Novel opsin gene variation in large-bodied, diurnal lemurs

Details on sample collection and opsin genotypin

Nucleotide alignment for exon 5 of the X-linked opsin gene (Indriidae)

Nucleotide alignment of consensus sequences for exon 5 of the X-linked opsin gene (Plain Text file in FASTA format generated in Geneious). Sequences represent 10 species of Indriidae