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Android Studio 3.3 Canary 8
Build #AI-182.3911.36.33.4978721, built on August 27, 2018
JRE: 1.8.0_152-release-1136-b06 x86_64
JVM: OpenJDK 64-Bit Server VM by JetBrains s.r.o
macOS 10.13.5
AGP version: 3.3.0-a08

The bundled proguard-android.txt file has the following:
# For native methods, see http://proguard.sourceforge.net/manual/examples.html#native
-keepclasseswithmembernames class * {
    native <methods>;
}

However, when obfuscating, the above doesn't prevent renaming/obfuscation of classes used in the arguments of the native methods. Hence, the above should be:

-keepclasseswithmembernames,includedescriptorclasses class * {
    native <methods>;
}

The file in question is at https://android.googlesource.com/platform/tools/base/+/studio-master-dev/build-system/gradle-core/src/main/resources/com/android/build/gradle/proguard-common.txt#15

For reference: https://www.guardsquare.com/en/products/proguard/manual/examples#native