First update of 2020

I’m writing this from my house in Canberra. A several weeks ago, we started hearing reports of the novel corona virus outbreak in Hubei province of China. Today, the virus, now known as COVID-19 (Corona Virus Disease 19) has swept across the world and the number of infections have continued to go up. However, the rate of infection in some countries appear to be going down. At the time of writing this, there are 786,876 infection worldwide.

The ANU has transitioned to remote working and online learning to adhere to “social distancing” rules. This is why I’m at home!

On a personal level, this year started quite well. I got to spend sometime at home, attended the World Congress of Herpetology 9 in Dunedin, New Zealand (Aotearoa), and visited the South Australian Museum (SAM) and the Western Australian Museum (WAM) before finding myself social distancing at home.

At the SAM and WAM, I was able to collect a lot of data for my thesis (on the evolution of blind snakes). This includes tissues from many species, body measurements, x-ray images, and photographs of head (for geometric morphometric analyses).

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View from my home office

The Research School will be closed until the end of June. I will be spending a lot of time at home. My plan is to finish up some old manuscripts, extract data from X-ray images, and come up with a plan to analyse my blind snake data!

 

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First two months at ANU

 

It’s been two months since I started my PhD here at the Australian National University! I’ve been reading quite a lot about Australian reptiles, especially elapid snakes (front-fanged venomous snakes). There are 107 terrestrial elapid snakes in Australia (according to AROD), which is a huge diversity, not to mention that many of the sea snakes are also elapids as well! More to come about my PhD project…

For now, I wanted to write a post highlighting a few things I’ve found useful as I review the literature in evolutionary biology, and things I’ve been doing on the side.

  • Reference manager: Zotero
    • Make sure to install Zotfile plug-in as this allow you to do more with your PDFs.
    • Organising your library with tags can be a very powerful way of archiving. Check out this tutorial.
  • Daily note taking: Evernote
  • In-depth note-taking: OneNote
    • I use OneNote to make more in-depth notes about papers I think will be important. For each paper I will note/record:
      • Main findings – you can get this by reading the abstract
      • Significance – how this paper will move the field?
      • Methods
      • Graphics – figures or photos of organism
    • I use OneNote because it lets me place figures where I want and draw things on them. Other software can do this too, I just use OneNote because I’m running a Windows machine.
  • Git: Bitbucket and Github
    • I learnt that Bitbucket offers private repository for free while Github does not. So I’ve been using Bitbucket as a private repo until I’m ready to publish my project on Github.
    • I also started learning how to use Git Bash (on windows). Bitbucket support page has some good documents to get you started.
  • R Markdown: making new CV with pagedown

The weather is warming up now in Canberra, it is lovely as always though.

HDTH

Kioloa, NSW and Mulligans Flat, ACT

Arrived in Australia about three weeks ago (it’s winter) and here are some animals I managed to photograph…

Kioloa, NSW

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Tawny frogmouth (Podargus strigoides)
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Haswell’s frog (Paracrinia haswelli) pair in amplexus

 

Mulligans Flat, ACT

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short-beaked echidna (Tachyglossus aculeatus)
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Eastern three-toed earless skink (Hemiergis talbingoensis)
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Red-necked wallaby (Macropus rufogriseus)

 

frog at night

I had a chance to explore a small pond around Aiken, South Carolina recently and found three species of frogs I can identify:

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Pine woods tree frog (Hyla fomerolis)
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American bullfrog (Lithobates climitans)
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American Green tree frog (Hyla cinearea)

 

There were numerous other frogs calling at night but I couldn’t find them.

Jamaica 2019

I graduated from Auburn at the end of 2018. Since, I’ve been spending time with my parents, visiting friends, and traveling.

Currently, I’m in Kingston (Jamaica) helping James Stroud a postdoctoral fellow in the Losos Lab set up his project on this wonderful island.

This is the first Caribbean country I’ve ever been to and it’s a privilege to see meet the people and see wildlife here. Among the fauna of interest are five species of anoles (in the Anolis or Norops genus if you go by Nicholson et al. 2018) and birds that cannot be found naturally elsewhere. Here are photos of (left) opalinus and (right) grahami:

Other species of anoles include lineatopus, valenciani (the twig anole baby picture below), and reconditus (this one we haven’t seen)!

 

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baby twig anole (valencienni)

I also spotted a Northern potoo (Nyctibius jamaicensis), which was very well camouflaged as a tree stump! Follow @derpetology on Instagram by Jon Suh for some fantastic photos of animals we found during this trip.

Miami trip and thesis defense

November is one of my favorite months.

The first week of November, one week before my thesis defense seminar, I went with my lab mate Josh back down to Miami to revisit my field site. It was great to see the lizards there again and gave me good opportunities to take pictures while Josh is catching anoles for his experiment.

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Puerto Rican crested anole female

We had a successful trip and was even able to squeeze a quick visit to the Everglades National Park the day after.

On the 8th November, I defended my thesis!

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I had a great time and I really appreciate everyone who came out to support!

summer 2018 updates

It’s the middle of the summer in Auburn, AL…

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This hatchling successfully hatched! It was alive.

This summer I’m running a lab experiment to test whether nest sites that urban-dwelling female crested anoles in Miami, FL use will yield higher survival than random sites.

How do we do this?
Last year I collected hourly temperature data by placing iButtons in random plots across suburban and nearby forest where crested anoles are abundant. These random plots either had eggs (nest plots) or did not (non-nest plots). When we examined these temperature more closely, we found that urban nest temperatures were warmer than those in the forests, which is not that surprising. However, within urban areas, temperatures in non-nest plot were markedly greater than nest plots and the extreme temperatures can reach 43°C and 39°C, respectively.

To test how these temperature affect developing embryos, we programmed our fancy incubators to mimic this 42-day natural cycle based on the temperature we observed in the field. We then allocate eggs to these treatments and wait to see if egg survival and hatchling phenotypes differ.

So that brings me to now…I’m waiting to see how many eggs will successfully hatch. If nest incubation treatments yield higher survival, mother lizards could really be a major reason why they are so successful, even in the Miami heat.

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Freshly laid eggs collected from our captive breeding colony
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Thanks MT for the help with processing eggs!

 

Field Work March 2018

The Warner Lab just wrapped up the first 2018 field trip. The main objectives for this trip include collecting lizards for Jenna’s project, taking way-point averages of trees on some of Dan’s islands, introducing our new post-doc Amelie to the study system, and clearing Tim’s CB1 and CB2 islands

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Dan saw an anole running under some rocks.

I was there for 6 days this time around and was involved with everything mentioned above. Well, I was primarily taking GPS coordinates for trees.

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Dewlapping male brown anole

 

It was also a reunion in many ways! 1) My friend Joe from Gonzaga visits and comes out to the field with us. 2) Tim Mitchell also joins the Warner Lab to wrap up his Crescent Beach project!

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Lunch break…peanut butter jelly sandwich.

Anolis Symposium 2018

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Phil, Jenna, I, and Josh representing the Warner Lab at the Anolis Symposium (PC: Jessica Pita)

We just got back from hot and tropical Miami this week with heaps of lizards! Last week three current and a former graduate student attended the 2018 Anolis Symposium at Fairchild Tropical Botanical Gardens. Hats off to the organizers, James Stroud and Anthony Geneva. Phil presented a poster on his recently published paper in Proceedings B about the benefit of early hatching. Jenna made a full debut in the lizard world with a side project testing potential effects of egg aggregation using brown anole eggs. Josh gave the final presentation summing up what we know about reproductive phenology in anoles and I gave a presentation on anole nest microenvironment differences between urban and forested sites.

After the symposium, we collected a bunch of lizards for a couple projects this summer. Stay tuned for updates! I met a lot of awesome scientists there and was very thankful to have the chance to talk to Sean Doody about eggs, Stu Nielsen about all sorts of herps, Colin Donihue about hurricanes, and many more!

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Female brown anole in suburban area
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Agama piticauda (Photo by Hannah G)
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Male brown anole flashing dewlap (PC: Hannah G)
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Very happy to retrieve an iButton buried 6 months ago!